Experiment: 5VL0

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/ml enzyme dialyzed against 50 mM ammonium N-[tris(hydroxylmethyl)methyl]2-aminoethane sulfonate (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM N-benzylformamide as the concentration of 2-methyl-2,4-pentanediol was raised to 25 %. Crystas was mounted on a fiber loop and flash vitrified by plunging it into liquid N2.

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.16	α = 90
b = 180.29	β = 106.18
c = 86.92	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	ADSC QUANTUM 210		2006-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.000	APS	17-ID

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	19.95	79.4	0.088	0.094	8.3	6.19		365139

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	1.24	59.5		0.513	0.576	1.7	4.34

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	1.2	19.95	361271	3775	79.39	0.1586	0.1582	0.16	0.1985	0.2	RANDOM	20.318

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]
1.63		0.19	-1.76		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.882
r_sphericity_free	19.85
r_dihedral_angle_4_deg	14.777
r_dihedral_angle_3_deg	11.714
r_sphericity_bonded	6.595
r_dihedral_angle_1_deg	6.266
r_rigid_bond_restr	3.996
r_angle_refined_deg	2.061
r_angle_other_deg	1.089
r_chiral_restr	0.128

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.882
r_sphericity_free	19.85
r_dihedral_angle_4_deg	14.777
r_dihedral_angle_3_deg	11.714
r_sphericity_bonded	6.595
r_dihedral_angle_1_deg	6.266
r_rigid_bond_restr	3.996
r_angle_refined_deg	2.061
r_angle_other_deg	1.089
r_chiral_restr	0.128
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
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	1357
Heterogen Atoms	240

Software

Software
Software Name	Purpose
d*TREK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
O	model building
d*TREK	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.