3RUP | pdb_00003rup

Crystal structure of E.coli biotin carboxylase in complex with two ADP and two Ca ions

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	PEG3350, CaCl2, pH 8.5, vapor diffusion, sitting drop, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.18	α = 90
b = 58.843	β = 94.24
c = 85.083	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD				M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A		NSLS	X4A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.99	84.82					56480

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.99	30	56444	2862	98.1	0.1736	0.1707	0.17	0.2269	0.23	RANDOM	20.6755

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]
0.1		0.41	0.81		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.568
r_dihedral_angle_4_deg	15.667
r_dihedral_angle_3_deg	13.884
r_dihedral_angle_1_deg	5.309
r_scangle_it	2.752
r_scbond_it	1.702
r_angle_refined_deg	1.312
r_mcangle_it	1.016
r_mcbond_it	0.648
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.568
r_dihedral_angle_4_deg	15.667
r_dihedral_angle_3_deg	13.884
r_dihedral_angle_1_deg	5.309
r_scangle_it	2.752
r_scbond_it	1.702
r_angle_refined_deg	1.312
r_mcangle_it	1.016
r_mcbond_it	0.648
r_nbtor_refined	0.297
r_nbd_refined	0.193
r_symmetry_hbond_refined	0.19
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.151
r_metal_ion_refined	0.13
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6854
Nucleic Acid Atoms
Solvent Atoms	905
Heterogen Atoms	115

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

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.