Experiment: 3EK1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OPX	pdb entry 2opx, modified

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	PROPLEX-96 F9: 1.0M AMMONIUM SULPHATE, 100MM MES PH 6.5, VAPOR DIFFUSION, TEMPERATURE 298K, pH 6.50, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.87	α = 92.03
b = 93.01	β = 107.58
c = 143.7	γ = 109.65

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	ADSC QUANTUM 315		2008-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.9999	ALS	5.0.2

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	2.1	50	94	0.061	0.061	11.02	1.81	246609	231828		-3	30.6

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)
	2.1	2.15	92.5		0.354	0.354	2.3	1.71	16866

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MR, MR	THROUGHOUT	pdb entry 2opx, modified	2.1	19.78	246609	231826	11634	94.2	0.164	0.164	0.161	0.16	0.225	0.22	RANDOM	19.83

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]
0.97	0.39	-0.19	-0.16	-0.35	-0.68

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.532
r_dihedral_angle_4_deg	16.63
r_dihedral_angle_3_deg	14.935
r_dihedral_angle_1_deg	6.11
r_scangle_it	4.181
r_scbond_it	2.613
r_angle_refined_deg	1.627
r_mcangle_it	1.432
r_angle_other_deg	0.967
r_mcbond_it	0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.532
r_dihedral_angle_4_deg	16.63
r_dihedral_angle_3_deg	14.935
r_dihedral_angle_1_deg	6.11
r_scangle_it	4.181
r_scbond_it	2.613
r_angle_refined_deg	1.627
r_mcangle_it	1.432
r_angle_other_deg	0.967
r_mcbond_it	0.8
r_mcbond_other	0.225
r_chiral_restr	0.096
r_bond_refined_d	0.018
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	28921
Nucleic Acid Atoms
Solvent Atoms	3142
Heterogen Atoms	136

Software

Software
Software Name	Purpose
BOS	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.