1WBQ | pdb_00001wbq

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

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. CRYOPROTECTED WITH 10-15% MPD., pH 8.30

Crystal Properties
Matthews coefficient	Solvent content
4.4	68.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.974	α = 90
b = 236.703	β = 106.14
c = 137.637	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	IMAGE PLATE	MARRESEARCH	OSMIC MIRRORS	2004-05-21	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	2.3	29.97	98.9	0.06	17.62	2.8		150167		-3.7	35.89

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	2.3	2.38	97.6		0.32	3.4	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	2.3	29.97	142654	7512	98.9	0.168	0.167	0.18	0.197	0.21	RANDOM	35.06

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]
1.45		0.94	-0.1		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.327
r_dihedral_angle_4_deg	16.933
r_dihedral_angle_3_deg	12.294
r_scangle_it	7.246
r_dihedral_angle_1_deg	5.706
r_scbond_it	5.156
r_mcangle_it	3.238
r_mcbond_it	2.57
r_angle_refined_deg	1.07
r_angle_other_deg	0.763
r_symmetry_vdw_other	0.265
r_symmetry_vdw_refined	0.199
r_nbd_refined	0.197
r_nbd_other	0.172
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.132
r_symmetry_hbond_refined	0.102
r_nbtor_other	0.079
r_chiral_restr	0.062
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
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	13964
Nucleic Acid Atoms
Solvent Atoms	832
Heterogen Atoms	14

Software

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