2V3Y | pdb_00002v3y

His361Ala Escherichia coli aminopeptidase P in complex with product

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WL9	PDB ENTRY 1WL9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	277	CRYSTALLISED IN 26% PEG 4K, 0.1 M TRIS PH 8.5 AT 277K. SOAKED IN 26% PEG 4K, 0.1 M TRIS PH 8.5, 1 MM MNCL2, 5 MM VAL-PRO-LEU, 10% MPD FOR 60 MIN AT 277K IMMEDIATELY PRIOR TO DATA COLLECTION.

Crystal Properties
Matthews coefficient	Solvent content
4.4	72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.132	α = 90
b = 177.132	β = 90
c = 96.17	γ = 120

Symmetry
Space Group	P 64 2 2

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	OSMIC MIRRORS	2005-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200H

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	1.6	65.1	99.9	0.07	21.2	7		116058		-3	19.28

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	1.6	1.69	100		0.45	3	4.6

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1WL9	1.6	154.3	112528	3514	99.8	0.154	0.154	0.16	0.167	RANDOM	10.22

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]
-0.18	-0.09		-0.18		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.62
r_dihedral_angle_4_deg	13.296
r_dihedral_angle_3_deg	11.292
r_dihedral_angle_1_deg	5.852
r_scangle_it	5.268
r_scbond_it	3.709
r_mcangle_it	2.273
r_mcbond_it	2.023
r_angle_refined_deg	1.304
r_angle_other_deg	0.901
r_symmetry_vdw_other	0.324
r_symmetry_vdw_refined	0.301
r_nbd_refined	0.216
r_nbd_other	0.194
r_nbtor_refined	0.174
r_symmetry_hbond_refined	0.157
r_xyhbond_nbd_refined	0.128
r_nbtor_other	0.083
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	3511
Nucleic Acid Atoms
Solvent Atoms	732
Heterogen Atoms	3

Software

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