Experiment: 3QKR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1II8	PDB ENTRY 1II8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	100 mM Tris, 200-300 mM lithium sulfate, 12-13% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.48	72.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.041	α = 90
b = 116.041	β = 90
c = 109.853	γ = 120

Symmetry
Space Group	P 61

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		2003-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	3.4	100	91.5	0.109	14.2	6.6	11608	10679	-3	-3

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)
	3.4	3.488	56.39		0.335	2	2.2

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 (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	PDB ENTRY 1II8	3.4	50	11648	10142	514	91.63	0.21432	0.21129	0.19	0.27444	0.25	RANDOM	99.954

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]
-0.73	-0.37		-0.73		1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	50.888
r_dihedral_angle_2_deg	40.306
r_scbond_it	40.055
r_mcangle_it	26.937
r_dihedral_angle_3_deg	20.621
r_mcbond_it	19.848
r_dihedral_angle_4_deg	16.647
r_dihedral_angle_1_deg	5.343
r_angle_refined_deg	1.031
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	50.888
r_dihedral_angle_2_deg	40.306
r_scbond_it	40.055
r_mcangle_it	26.937
r_dihedral_angle_3_deg	20.621
r_mcbond_it	19.848
r_dihedral_angle_4_deg	16.647
r_dihedral_angle_1_deg	5.343
r_angle_refined_deg	1.031
r_nbtor_refined	0.304
r_symmetry_hbond_refined	0.249
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.169
r_symmetry_vdw_refined	0.169
r_chiral_restr	0.069
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3339
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	10

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.