4MKT | pdb_00004mkt

Human Leukotriene A4 Hydrolase in complex with Pro-Gly-Pro analogue and 4-(4-benzylphenyl)thiazol-2-amine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DPR	PDB ENTRY 4DPR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIQUID DIFFUSION	7	277	50 mM Sodium Acetate, 22% (v/v) PEG 8000, 5 mM YbCl3, pH 7.0, LIQUID DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.809	α = 90
b = 87.588	β = 90
c = 100.056	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	PIXEL	PSI PILATUS 6M	Mirrors	2013-04-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918	BESSY	14.1

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	1.618	43.79	99.7	0.098	13.51	6.61	86651	86391			26.45

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	1.618	1.72	98.8		1	1.96

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4DPR	1.618	43.79	82284	82070	4320	99.74	0.15784	0.15784	0.15597	0.16	0.19294	0.2	RANDOM	20.317

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]
-0.13			-1.67		1.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.578
r_dihedral_angle_4_deg	17.676
r_dihedral_angle_3_deg	14.015
r_dihedral_angle_1_deg	6.067
r_angle_refined_deg	2.072
r_angle_other_deg	1.013
r_chiral_restr	0.131
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.578
r_dihedral_angle_4_deg	17.676
r_dihedral_angle_3_deg	14.015
r_dihedral_angle_1_deg	6.067
r_angle_refined_deg	2.072
r_angle_other_deg	1.013
r_chiral_restr	0.131
r_bond_refined_d	0.021
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4860
Nucleic Acid Atoms
Solvent Atoms	635
Heterogen Atoms	49

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

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.