Experiment: 5VN1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P1R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	7	278	10 mg protein/ml dialyzed against 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonate buffer, pH 7 (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM (racemic) (R,S)-N-1-methylhexylformamide as the concentration of 2-methyl-2,4-pentanediol was raised to 25%. Crystal on loop plunged into liquid N2.

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.212	α = 90
b = 180.808	β = 106.12
c = 86.841	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	CCD	MAR CCD 165 mm		1999-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.936	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.2	20	83.8	0.122	0.151	5.77	1.762		386016		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.25	67.5		0.318	0.426	2.2	1.518

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	1p1r	1.25	20	325043	1650	80.01	0.1517	0.1515	0.15	0.1866	0.19	RANDOM	25.461

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]
1.71		0.28	-1.4		-0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.372
r_sphericity_free	18.984
r_dihedral_angle_4_deg	14.312
r_dihedral_angle_3_deg	11.536
r_sphericity_bonded	7.418
r_dihedral_angle_1_deg	6.276
r_rigid_bond_restr	2.976
r_angle_refined_deg	1.885
r_angle_other_deg	1.063
r_chiral_restr	0.122

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.372
r_sphericity_free	18.984
r_dihedral_angle_4_deg	14.312
r_dihedral_angle_3_deg	11.536
r_sphericity_bonded	7.418
r_dihedral_angle_1_deg	6.276
r_rigid_bond_restr	2.976
r_angle_refined_deg	1.885
r_angle_other_deg	1.063
r_chiral_restr	0.122
r_bond_refined_d	0.017
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11140
Nucleic Acid Atoms
Solvent Atoms	1329
Heterogen Atoms	250

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
X-PLOR	phasing
O	model building

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.