Experiment: 3LBK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	300	0.1M sodium-acetate-trihydrate, 2M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.46	α = 90
b = 60.46	β = 90
c = 48.05	γ = 90

Symmetry
Space Group	P 41 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	CCD	MAR CCD 165 mm	monochromator, mirror	2009-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00	SLS	X10SA

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	2.2	30	88.6	0.079	12.1		7896	6949	2	2

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)
	2.2	2.3	80.4		0.502	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1RV1	2.3	20	2	6949	6613	323	88.61	0.21	0.20942	0.20745	0.22	0.25145	0.28	RANDOM	39.097

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]
1.28			1.28		-2.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.586
r_dihedral_angle_4_deg	28.761
r_dihedral_angle_3_deg	20.756
r_dihedral_angle_1_deg	7.597
r_scangle_it	3.169
r_scbond_it	1.896
r_angle_refined_deg	1.695
r_mcangle_it	1.59
r_angle_other_deg	0.948
r_mcbond_it	0.868

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.586
r_dihedral_angle_4_deg	28.761
r_dihedral_angle_3_deg	20.756
r_dihedral_angle_1_deg	7.597
r_scangle_it	3.169
r_scbond_it	1.896
r_angle_refined_deg	1.695
r_mcangle_it	1.59
r_angle_other_deg	0.948
r_mcbond_it	0.868
r_mcbond_other	0.129
r_chiral_restr	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	695
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms	37

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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.