Experiment: 5ZRX

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KKA	3KKA and 2K4P
experimental model	PDB	2K4P	3KKA and 2K4P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	289	0.2M Succinic acid pH 7.0, 20% w/v Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2	38.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.283	α = 90
b = 43.344	β = 95.35
c = 46.377	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	100	CCD	ADSC QUANTUM 315r		2014-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97915	SSRF	BL17U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.5	50	99	0.047	0.056	0.029	14.9	3.6		43485

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	1.5	1.53	98.1		0.624	0.736	0.386	0.87		3.5

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	3KKA and 2K4P	1.5	50	41294	2188	98.79	0.1458	0.1434	0.15	0.1911	0.19	RANDOM	31.151

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]
0.18		-0.66	0.7		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.197
r_sphericity_free	29.589
r_dihedral_angle_4_deg	14.747
r_dihedral_angle_3_deg	13.456
r_sphericity_bonded	13.133
r_dihedral_angle_1_deg	4.549
r_rigid_bond_restr	1.395
r_angle_refined_deg	1.224
r_angle_other_deg	0.953
r_chiral_restr	0.076

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.197
r_sphericity_free	29.589
r_dihedral_angle_4_deg	14.747
r_dihedral_angle_3_deg	13.456
r_sphericity_bonded	13.133
r_dihedral_angle_1_deg	4.549
r_rigid_bond_restr	1.395
r_angle_refined_deg	1.224
r_angle_other_deg	0.953
r_chiral_restr	0.076
r_bond_refined_d	0.009
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	2007
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms

Software

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