Experiment: 5GJD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.7	293	1.7M sodium potassium phosphate, 20%(v/v) Glycerol as cryoprotectant

Crystal Properties
Matthews coefficient	Solvent content
3.85	68.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.96	α = 90
b = 132.37	β = 90
c = 142.68	γ = 90

Symmetry
Space Group	I 2 2 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	RAYONIX MX-225		2008-07-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0000	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.79	53.7	99.6	0.109	0.997	11.8	5.3		14035

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.79	2.86	100		1.173	0.561		5.4

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	2EVA	2.79	53.7	13351	684	99.61	0.2006	0.1984	0.2451	RANDOM	74.242

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]
-5.41			-2.36		7.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.402
r_dihedral_angle_4_deg	14.679
r_dihedral_angle_3_deg	14.38
r_dihedral_angle_1_deg	6.137
r_mcangle_it	5.431
r_mcbond_it	3.201
r_mcbond_other	3.189
r_angle_refined_deg	1.216
r_angle_other_deg	0.869
r_chiral_restr	0.066

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.402
r_dihedral_angle_4_deg	14.679
r_dihedral_angle_3_deg	14.38
r_dihedral_angle_1_deg	6.137
r_mcangle_it	5.431
r_mcbond_it	3.201
r_mcbond_other	3.189
r_angle_refined_deg	1.216
r_angle_other_deg	0.869
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2245
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	37

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.