2BH3 | pdb_00002bh3

Zn 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		7	277	AMINOPEPTIDASE P WAS DIALYSED AGAINST EGTA PRIOR TO CRYSTALLISATION. CRYSTALS WERE GROWN IN 26% MPD, 100 MM NACITRATE (PH 7.0) AND 200 MM MGACETATE AT 4C. CRYSTALS WERE SOAKED FOR 2 HOURS IN RESERVOIR SOLUTION SUPPLEMENTED WITH 1 MM ZNCL2 AND 10 MM PROLEU DIPEPTIDE PRIOR TO DATA COLLECTION.

Crystal Properties
Matthews coefficient	Solvent content
5.32	76.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.012	α = 90
b = 138.012	β = 90
c = 230.734	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	2004-12-11	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	2.4	60	99.2	0.05	25.2	6.1		43466		-3	55.02

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	2.4	2.49	98.5		0.52	3.2	5

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	2.4	60.19	41151	2099	98.8	0.175	0.174	0.18	0.201	0.21	RANDOM	47.17

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]
1.58			1.58		-3.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.372
r_dihedral_angle_4_deg	16.164
r_dihedral_angle_3_deg	12.067
r_dihedral_angle_1_deg	6.055
r_scangle_it	3.879
r_scbond_it	2.522
r_mcangle_it	1.542
r_mcbond_it	1.131
r_angle_refined_deg	1.117
r_angle_other_deg	0.755
r_symmetry_vdw_other	0.269
r_symmetry_vdw_refined	0.245
r_nbd_refined	0.193
r_nbd_other	0.17
r_nbtor_refined	0.169
r_symmetry_hbond_refined	0.133
r_xyhbond_nbd_refined	0.117
r_nbtor_other	0.081
r_chiral_restr	0.063
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	3487
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	34

Software

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