Experiment: 5K5B

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.95	293	sodium acetate, PEG 400, DTT, 2-methyl-2, 4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.76	α = 90
b = 54.28	β = 92.2
c = 70.15	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	PIXEL	DECTRIS PILATUS 6M-F		2014-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.972957	ESRF	ID23-1

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	1.35	46.97	98.1	0.036	0.999	18.37	4.36		75872		-3	25.092

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	1.35	1.38	95.7		0.56	2.31	4.23

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	4Q0H	1.35	39.37	72086	3795	98.07	0.1422	0.1407	0.1709	RANDOM	25.474

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]
0.08		-0.2			-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.039
r_sphericity_free	30.668
r_sphericity_bonded	13.888
r_dihedral_angle_4_deg	12.91
r_dihedral_angle_3_deg	11.684
r_dihedral_angle_1_deg	6.327
r_mcangle_it	2.235
r_scbond_it	2.134
r_mcbond_it	1.675
r_rigid_bond_restr	1.654

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.039
r_sphericity_free	30.668
r_sphericity_bonded	13.888
r_dihedral_angle_4_deg	12.91
r_dihedral_angle_3_deg	11.684
r_dihedral_angle_1_deg	6.327
r_mcangle_it	2.235
r_scbond_it	2.134
r_mcbond_it	1.675
r_rigid_bond_restr	1.654
r_angle_refined_deg	1.506
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2335
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms	63

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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 R01GM133198.