1ZSV

Crystal structure of human NADP-dependent leukotriene B4 12-hydroxydehydrogenase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1V3V	1V3V.pdb

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	PEG3350, NaI, ethylene glycol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.543	α = 90
b = 92.543	β = 90
c = 202.77	γ = 90

Symmetry
Space Group	P 43

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	MARMOSAIC 225 mm CCD		2005-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.98402	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	67.57	99.4	0.139			74944	74944

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.42	97.1

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	1V3V.pdb	2.3	62.3	72302	72302	1920	98.42	0.1969	0.1969	0.19511	0.24933	RANDOM	43.497

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]
-0.55			-0.55		1.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.289
r_dihedral_angle_3_deg	16.573
r_dihedral_angle_4_deg	15.973
r_dihedral_angle_1_deg	7.384
r_scangle_it	7.035
r_scbond_it	5.181
r_mcangle_it	2.905
r_mcbond_it	1.991
r_angle_refined_deg	1.618
r_angle_other_deg	0.843
r_mcbond_other	0.523
r_nbd_refined	0.19
r_nbtor_refined	0.175
r_nbd_other	0.169
r_symmetry_vdw_other	0.159
r_xyhbond_nbd_refined	0.156
r_symmetry_vdw_refined	0.152
r_chiral_restr	0.088
r_nbtor_other	0.088
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9834
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing