Experiment: 4DK4

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	290	25% w/v PEG1500, 0.1 M PCB buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
1.73	29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.84	α = 90
b = 83.19	β = 90
c = 91.18	γ = 90

Symmetry
Space Group	P 21 21 21

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 4		2010-06-12		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.9	61.455	100	0.107	0.107	13.2	8.3	36008	36008	1	1	19.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	100		0.544	0.544	1.4	7.3	5150

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1OGK	1.9	61.455	36008	35890	1793	99.82	0.1801	0.1801	0.1774	0.2321	RANDOM	22.5685

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]
-0.65			0.66		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.597
r_scbond_it	31.334
r_scangle_it	17.995
r_mcangle_it	15.028
r_dihedral_angle_4_deg	13.052
r_mcbond_it	12.662
r_dihedral_angle_3_deg	11.806
r_dihedral_angle_1_deg	5.28
r_angle_refined_deg	1.434
r_angle_other_deg	0.982

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.597
r_scbond_it	31.334
r_scangle_it	17.995
r_mcangle_it	15.028
r_dihedral_angle_4_deg	13.052
r_mcbond_it	12.662
r_dihedral_angle_3_deg	11.806
r_dihedral_angle_1_deg	5.28
r_angle_refined_deg	1.434
r_angle_other_deg	0.982
r_mcbond_other	0.413
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3364
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	54

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX	data collection

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.