1W7V | pdb_00001w7v

ZnMg substituted aminopeptidase P from E. coli

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 WITH ALL HET ATOMS, WATERS AND MULTIPLE CONFORMERS REMOVED

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.3		ROOM TEMPERATURE HANGING DROP WITH 16% PEG4K, 0.1 M TRIS (PH8.3), 0.2 M MGCL2. TRANSFERRED TO A DROP ABOVE CONDITIONS PLUS WITH 10 MM VAL-PRO-LEU PEPTIDE AND ALLOWED TO EQUILIBRATE OVERNIGHT., pH 8.30

Crystal Properties
Matthews coefficient	Solvent content
4.4	71.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.731	α = 90
b = 236.527	β = 106.34
c = 137.997	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC CCD	MIRROR	2004-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		SSRL	BL9-2

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	40	97.9	0.07	13.9	2.9		225729		-3	32.21

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	2.07	96.3		0.44	6	2.7

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 1WL9 WITH ALL HET ATOMS, WATERS AND MULTIPLE CONFORMERS REMOVED	2	37.8	214328	11297	97.9	0.157	0.156	0.17	0.18	0.19	RANDOM	36.28

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]
2.04		1.44	-0.15		-1.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.13
r_dihedral_angle_4_deg	16.981
r_dihedral_angle_3_deg	12.084
r_scangle_it	8.978
r_scbond_it	5.879
r_dihedral_angle_1_deg	5.501
r_mcangle_it	3.689
r_mcbond_it	3.189
r_angle_refined_deg	1.106
r_angle_other_deg	0.762
r_symmetry_vdw_other	0.248
r_symmetry_vdw_refined	0.23
r_nbd_refined	0.2
r_nbd_other	0.177
r_nbtor_refined	0.172
r_symmetry_hbond_refined	0.144
r_xyhbond_nbd_refined	0.126
r_nbtor_other	0.08
r_chiral_restr	0.065
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
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	14028
Nucleic Acid Atoms
Solvent Atoms	1094
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing