Experiment: 3NVY

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Sitting Batch	7.2	298	PEG 8000, pH 7.2, Sitting Batch, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.686	α = 90
b = 73.398	β = 97.13
c = 138.21	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		CCD	MAR CCD 165 mm		2010-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.9793	APS	31-ID

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	2	101.5	98.2				178392		2

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	2	2.052	98.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2	101.5	175239	8835	98.23	0.194	0.1917	0.19	0.2375	0.24	RANDOM	26.7408

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]
-2.67		-0.41	0.58		1.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.437
r_dihedral_angle_4_deg	17.684
r_dihedral_angle_3_deg	15.988
r_dihedral_angle_1_deg	6.327
r_scangle_it	3.63
r_scbond_it	2.366
r_angle_refined_deg	1.554
r_mcangle_it	1.426
r_mcbond_it	0.908
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.437
r_dihedral_angle_4_deg	17.684
r_dihedral_angle_3_deg	15.988
r_dihedral_angle_1_deg	6.327
r_scangle_it	3.63
r_scbond_it	2.366
r_angle_refined_deg	1.554
r_mcangle_it	1.426
r_mcbond_it	0.908
r_nbtor_refined	0.308
r_symmetry_vdw_refined	0.284
r_symmetry_hbond_refined	0.255
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19122
Nucleic Acid Atoms
Solvent Atoms	1057
Heterogen Atoms	222

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
CCP4	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.