Experiment: 6SRD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WU4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	291	23% PEG 6K, 0.1 M Tris pH 8.0, 0.2 M NaCl, 0.01 M Hexammine cobalt (III) chrloride. Soaking experiment in the precipitant solution supplemented with 50 mM xylose. Cryoprotectan solution consisting of mother liquor plus 25% (v/v) glycerol.

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.566	α = 87.83
b = 59.153	β = 77.98
c = 79.534	γ = 74.33

Symmetry
Space Group	P 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	KB Mirrors	2015-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	1.041910	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.93	48.63	96.4	0.125	0.148	0.078	0.992	7.2	3.5		64154

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	1.93	1.98	93.2		0.723	0.879	0.489	0.663	2	3.1

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	1WU4	1.93	48.63	60880	3260	96.37	0.1909	0.1889	0.2	0.2286	0.23	RANDOM	16.208

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]
0.85	1.09	0.4	0.31	-0.74	-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.951
r_dihedral_angle_4_deg	15.632
r_dihedral_angle_3_deg	12.641
r_dihedral_angle_1_deg	6.787
r_angle_refined_deg	1.418
r_angle_other_deg	1.362
r_chiral_restr	0.076
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.951
r_dihedral_angle_4_deg	15.632
r_dihedral_angle_3_deg	12.641
r_dihedral_angle_1_deg	6.787
r_angle_refined_deg	1.418
r_angle_other_deg	1.362
r_chiral_restr	0.076
r_gen_planes_refined	0.006
r_bond_refined_d	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	6226
Nucleic Acid Atoms
Solvent Atoms	613
Heterogen Atoms	44

Software

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