Experiment: 3ROK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YH3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	0.1M sodium acetate pH4.0, 0.2M ammonium acetate, 3% isopropanol, 15% PEG10000, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.87	α = 109.56
b = 53.658	β = 90.95
c = 63.562	γ = 94.73

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	CCD	RAYONIX MX-225		2010-03-31	M	SINGLE WAVELENGTH
2	1
3	1
4	1
5	1
6	1
7	1
8	1
9	1
10	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97908	SSRF	BL17U

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	1.65	50	95.9	0.071	14.4	3.9		59566

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	1.65	1.71	95.5		0.399		4	5944

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	1YH3	1.65	50	59515	3006	95.34	0.1812	0.1798	0.2088	RANDOM	33.447

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]
-1.17	-0.02	0.11	0.41	0.61	1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.864
r_dihedral_angle_4_deg	14.631
r_dihedral_angle_3_deg	12.826
r_dihedral_angle_1_deg	5.512
r_scangle_it	3.022
r_scbond_it	1.961
r_angle_refined_deg	1.282
r_mcangle_it	1.145
r_angle_other_deg	0.816
r_mcbond_it	0.574

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.864
r_dihedral_angle_4_deg	14.631
r_dihedral_angle_3_deg	12.826
r_dihedral_angle_1_deg	5.512
r_scangle_it	3.022
r_scbond_it	1.961
r_angle_refined_deg	1.282
r_mcangle_it	1.145
r_angle_other_deg	0.816
r_mcbond_it	0.574
r_mcbond_other	0.157
r_chiral_restr	0.138
r_bond_refined_d	0.009
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	4082
Nucleic Acid Atoms
Solvent Atoms	368
Heterogen Atoms	34

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	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 R01GM157729.