5L31 | pdb_00005l31

Crystal structure of an engineered metal-free RIDC1 variant containing five disulfide bonds.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JEA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	Drop consists of 1 uL of 45% MPD, and 0.1 M Bis Tris (pH 6.5) mixed with 1.5 uL of 2.8 mM protein

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.594	α = 90
b = 77.534	β = 90
c = 88.063	γ = 90

Symmetry
Space Group	P 21 21 21

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 325 mm CCD		2016-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.98	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	2.4	38.77	99.8	0.067	14.9	6.9		17325

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53	99.4		0.23	5.7	7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	4JEA	2.4	38.77	16402	866	99.61	0.22716	0.22501	0.23	0.26701	0.27	RANDOM	56.147

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]
0.29			1.32		-1.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	46.128
r_dihedral_angle_3_deg	16.997
r_dihedral_angle_4_deg	10.03
r_dihedral_angle_1_deg	5.041
r_mcangle_it	3.051
r_mcbond_it	1.809
r_mcbond_other	1.807
r_angle_refined_deg	1.302
r_angle_other_deg	0.983
r_chiral_restr	0.062

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	46.128
r_dihedral_angle_3_deg	16.997
r_dihedral_angle_4_deg	10.03
r_dihedral_angle_1_deg	5.041
r_mcangle_it	3.051
r_mcbond_it	1.809
r_mcbond_other	1.807
r_angle_refined_deg	1.302
r_angle_other_deg	0.983
r_chiral_restr	0.062
r_gen_planes_other	0.009
r_bond_refined_d	0.008
r_bond_other_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3222
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	174

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

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.