5EVZ

Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with ADP and inorganic phosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EXW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	289	24-26% PEG3350, 0.1 M Tris-HCl, 0.2 M sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.55	α = 90
b = 74.802	β = 98.6
c = 89.22	γ = 90

Symmetry
Space Group	P 1 21 1

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	RAYONIX MX-300		2015-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.82	50	99.9	0.077	13.4	5		64199

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	1.82	1.85	99.9		0.457		4.6	3191

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5EXW	1.85	44.31	58565	3120	99.83	0.1674	0.1654	0.2053	RANDOM	32.051

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]
1.21		-1.12	-0.45		-0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.574
r_dihedral_angle_4_deg	15.189
r_dihedral_angle_3_deg	11.873
r_dihedral_angle_1_deg	5.227
r_mcangle_it	1.656
r_angle_refined_deg	1.34
r_mcbond_it	1.157
r_mcbond_other	1.152
r_angle_other_deg	0.727
r_chiral_restr	0.071

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.574
r_dihedral_angle_4_deg	15.189
r_dihedral_angle_3_deg	11.873
r_dihedral_angle_1_deg	5.227
r_mcangle_it	1.656
r_angle_refined_deg	1.34
r_mcbond_it	1.157
r_mcbond_other	1.152
r_angle_other_deg	0.727
r_chiral_restr	0.071
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5920
Nucleic Acid Atoms
Solvent Atoms	534
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MOLREP	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.