2QR5 | pdb_00002qr5

Aeropyrum pernix acylaminoacyl peptidase, H367A mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VE6	PDB ENTRY 1VE6 (ONE MONOMER)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.35	293	169 mM sodium acetate, 0.4 mM EDTA, 2% PEG 4000 0.51% beta-octyl-glucoside, pH 6.35, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.27	α = 90
b = 105.04	β = 90
c = 114.02	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	293	IMAGE PLATE	RIGAKU RAXIS IIC		2006-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	20	93.2	0.118	11.5	3.71		58729		-3	38.14

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.5	93.6		0.467	0.467	3.61	3.42	18581

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 1VE6 (ONE MONOMER)	2.2	19.69	55723	55723	2982	93.34	0.17959	0.17959	0.17739	0.17	0.22225	0.22	RANDOM	35.778

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]
0.01			0.01		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.37
r_dihedral_angle_4_deg	21.238
r_dihedral_angle_3_deg	16.015
r_dihedral_angle_1_deg	6.954
r_scangle_it	3.067
r_mcangle_it	2.457
r_scbond_it	2.052
r_mcbond_it	1.592
r_angle_refined_deg	1.502
r_nbtor_refined	0.314
r_symmetry_hbond_refined	0.276
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.157
r_symmetry_vdw_refined	0.109
r_chiral_restr	0.091
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8657
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms

Software

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