2BHD | pdb_00002bhd

Mg substituted E. 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	1N51	PDB ENTRY 1N51 STRIPPED OF MULTIPLE CONFORMERS, SOLVENT ATOMS AND HETERO COMPOUNDS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	AMINOPEPTIDASE P WAS DIALYSED AGAINST EGTA PRIOR TO CRYSTALLISATION. CRYSTALS WERE GROWN USING HANGING DROP VAOPR DIFFUSION AT 4C. RESERVOIR CONTAINED 26% MPD, 100 MM NA.CITRATE (PH 7.5) AND 200 MM MG.ACETATE. CRYSTALS WERE SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 10 MM VALPROLEU TRIPEPTIDE FOR 20 HOURS AT 4C PRIOR TO DATA COLLECTION.

Crystal Properties
Matthews coefficient	Solvent content
5.6	77.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.569	α = 90
b = 138.569	β = 90
c = 230.962	γ = 90

Symmetry
Space Group	I 41 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	2004-10-28	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	2.5	60	99.2	0.09	22.7	7.8		38892		-3	55.48

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	2.5	2.59	100		0.58	3.4	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 1N51 STRIPPED OF MULTIPLE CONFORMERS, SOLVENT ATOMS AND HETERO COMPOUNDS	2.5	60.19	36971	1888	99.2	0.18	0.179	0.19	0.204	0.21	RANDOM	43.16

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]
1.57			1.57		-3.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.273
r_dihedral_angle_4_deg	16.289
r_dihedral_angle_3_deg	12.058
r_dihedral_angle_1_deg	5.687
r_scangle_it	2.696
r_scbond_it	1.723
r_angle_refined_deg	1.169
r_mcangle_it	1.101
r_mcbond_it	0.75
r_angle_other_deg	0.743
r_symmetry_vdw_other	0.275
r_symmetry_vdw_refined	0.271
r_nbd_refined	0.212
r_nbtor_refined	0.174
r_nbd_other	0.167
r_xyhbond_nbd_refined	0.121
r_symmetry_hbond_refined	0.113
r_nbtor_other	0.079
r_chiral_restr	0.064
r_bond_refined_d	0.01
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	3503
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	16

Software

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