Experiment: 3DLZ

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VUW	PDB entry 2VUW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.2M Li2SO4, 0.1M HEPES pH 7.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.315	α = 90
b = 49.729	β = 90
c = 98.009	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	IMAGE PLATE	RIGAKU RAXIS IV		2008-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54178

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	1.85	41.169	99.1	0.087	0.087	9.3	2.9	31316	30974

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	1.85	1.95	97.6		0.512	0.512	2	2.8	4362

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 2VUW	1.85	41.169	30934	30934	1558	98.78	0.167	0.167	0.164	0.216	RANDOM	22.131

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]
-0.3			0.82		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.152
r_dihedral_angle_3_deg	12.554
r_dihedral_angle_4_deg	12.297
r_dihedral_angle_1_deg	6.543
r_scangle_it	3.673
r_scbond_it	2.275
r_angle_refined_deg	1.545
r_mcangle_it	1.459
r_angle_other_deg	0.975
r_mcbond_it	0.839

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.152
r_dihedral_angle_3_deg	12.554
r_dihedral_angle_4_deg	12.297
r_dihedral_angle_1_deg	6.543
r_scangle_it	3.673
r_scbond_it	2.275
r_angle_refined_deg	1.545
r_mcangle_it	1.459
r_angle_other_deg	0.975
r_mcbond_it	0.839
r_mcbond_other	0.233
r_chiral_restr	0.093
r_bond_refined_d	0.016
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	2629
Nucleic Acid Atoms
Solvent Atoms	462
Heterogen Atoms	32

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

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.