Experiment: 3KRV

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R61

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	0.2M LiSulfate, 0.1M TrisH8.5, 1.26M AmmSulfate freezing cond: 20% ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
4.78	74.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.096	α = 90
b = 119.096	β = 90
c = 124.413	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	SBC-3		2007-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.979	APS	19-BM

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	2.55	50	99.9	0.072	0.072	39.3	8.4		29938		-5

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	2.55	2.64	100		0.688	0.688	2.772	8.2	2935

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	1R61	2.55	34.88	28852	961	99.67	0.19434	0.19273	0.24435	RANDOM	28.582

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]
0.29			0.29		-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.845
r_dihedral_angle_4_deg	17.558
r_dihedral_angle_3_deg	14.109
r_dihedral_angle_1_deg	6.298
r_scangle_it	3.938
r_scbond_it	2.505
r_angle_refined_deg	1.667
r_mcangle_it	1.515
r_mcbond_it	0.917
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.845
r_dihedral_angle_4_deg	17.558
r_dihedral_angle_3_deg	14.109
r_dihedral_angle_1_deg	6.298
r_scangle_it	3.938
r_scbond_it	2.505
r_angle_refined_deg	1.667
r_mcangle_it	1.515
r_mcbond_it	0.917
r_nbtor_refined	0.313
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.172
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.111
r_symmetry_hbond_refined	0.096
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3174
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	65

Software

Software
Software Name	Purpose
HKL-3000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.