Experiment: 1XVY

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XVX	pdb entry 1xvx

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	273	lithium chloride, PEG 6000, citric acid, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.046	α = 90
b = 65.392	β = 111.9
c = 50.266	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	RIGAKU		2004-07-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.74	24.88	99.2				27910

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.74	1.8	95.6

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 1xvx	1.74	46.63	27026	26494	1414	98.03	0.165	0.16495	0.16248	0.20927	RANDOM	12.729

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]
-0.37		-0.47	0.03		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.75
r_dihedral_angle_4_deg	12.901
r_dihedral_angle_3_deg	12.289
r_dihedral_angle_1_deg	5.585
r_scangle_it	3.437
r_scbond_it	2.24
r_angle_refined_deg	1.304
r_mcangle_it	1.135
r_mcbond_it	0.721
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.75
r_dihedral_angle_4_deg	12.901
r_dihedral_angle_3_deg	12.289
r_dihedral_angle_1_deg	5.585
r_scangle_it	3.437
r_scbond_it	2.24
r_angle_refined_deg	1.304
r_mcangle_it	1.135
r_mcbond_it	0.721
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.228
r_nbd_refined	0.203
r_symmetry_hbond_refined	0.153
r_xyhbond_nbd_refined	0.117
r_chiral_restr	0.086
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2334
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
CCP4	data scaling
MOLREP	phasing

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.