2Y05

Crystal structure of human leukotriene B4 12-hydroxydehydrogenase in complex with NADP and raloxifene

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				10% PEG 10K, 8% ETGLY, 0.1M HEPES, PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.274	α = 90
b = 116.599	β = 90
c = 154.607	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH		2008-07-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		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	2.2	59.5	95	0.09	5.9	3.9		82606		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	96.4		0.52	2.6	3.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1ZSV	2.2	59.55	77068	4025	94.08	0.1957	0.19383	0.23085	RANDOM	22.235

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]
0.15			-0.21		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.048
r_dihedral_angle_4_deg	14.386
r_dihedral_angle_3_deg	13.835
r_dihedral_angle_1_deg	6.114
r_scangle_it	5.989
r_scbond_it	4.033
r_mcangle_it	2.507
r_mcbond_it	1.463
r_angle_refined_deg	1.43
r_angle_other_deg	0.87
r_mcbond_other	0.644
r_chiral_restr	0.078
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9909
Nucleic Acid Atoms
Solvent Atoms	438
Heterogen Atoms	301

Software

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