4ZNZ | pdb_00004znz

Crystal structure of Escherichia coli carbonic anhydrase (YadF) in complex with Zn - artifact of purification

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.3 ul of 7.4 mg/ml protein in 50 mM TRIS pH 7.9, 200 mM NaCl and 0.5 mM TCEP were mixed with the 0.3 ul of SaltRx condition #96 (60% v/v Tacsimate pH 7.0 and 0.1 M BIS-TRIS propane pH 7.0) and equilibrated against SaltRx condition #96 solution in 96 Well 3 drop Crystallization Plate (Swissci)

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.909	α = 90
b = 67.909	β = 90
c = 84.93	γ = 90

Symmetry
Space Group	P 42 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Bimorph K-B pair	2013-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.27822	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.7	50	93.6	0.122	0.122	0.13	0.045	6.5	8.1	5907	5527		-3	58.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.75	95.8		0.926	0.988	0.338	0.752	1.8	8.1	276

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.7	50	5247	255	93.83	0.1534	0.1488	0.16	0.2575	0.25	RANDOM	53.775

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.68			0.68		-1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.181
r_dihedral_angle_4_deg	18.761
r_dihedral_angle_3_deg	15.992
r_dihedral_angle_1_deg	6.888
r_mcangle_it	6.404
r_mcbond_it	4.165
r_mcbond_other	4.129
r_angle_refined_deg	1.591
r_angle_other_deg	0.998
r_chiral_restr	0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.181
r_dihedral_angle_4_deg	18.761
r_dihedral_angle_3_deg	15.992
r_dihedral_angle_1_deg	6.888
r_mcangle_it	6.404
r_mcbond_it	4.165
r_mcbond_other	4.129
r_angle_refined_deg	1.591
r_angle_other_deg	0.998
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1674
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	phasing
MLPHARE	phasing
SHELX	phasing
HKL-3000	data scaling
HKL-3000	data reduction
BLU-MAX	data collection
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.