2VZK | pdb_00002vzk

Structure of the acyl-enzyme complex of an N-terminal nucleophile (Ntn) hydrolase, OAT2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VZ6	PDB ENTRY 1VZ6, CHAIN A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	290	1.4M AMMONIUM SULPHATE, 100MM N-ACETYL-L-GLUTAMATE, 200MM NACL, 100MM TRIS HCL PH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.273	α = 90
b = 73.878	β = 92.71
c = 172.166	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	IMAGE PLATE	MARRESEARCH	MONTEL	2007-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR

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	2.33	37	94.2	0.12	6.4	3.7		62183			51

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	2.33	2.45	97.9		0.7	2.03	3.7

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	PDB ENTRY 1VZ6, CHAIN A	2.33	171.5	58750	3048	93.66	0.25538	0.25386	0.25	0.28432	0.28	RANDOM	22.038

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]
1.41		-1.98	-1		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.576
r_dihedral_angle_4_deg	23.531
r_dihedral_angle_3_deg	17.326
r_dihedral_angle_1_deg	8.785
r_scangle_it	2.909
r_scbond_it	1.811
r_angle_refined_deg	1.713
r_angle_other_deg	1.331
r_mcangle_it	0.916
r_mcbond_it	0.768
r_symmetry_vdw_other	0.302
r_nbd_refined	0.243
r_symmetry_vdw_refined	0.243
r_symmetry_hbond_refined	0.227
r_nbd_other	0.221
r_xyhbond_nbd_refined	0.193
r_nbtor_refined	0.179
r_chiral_restr	0.168
r_nbtor_other	0.093
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.003
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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	11211
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing