1W2M

Ca-substituted form of E. coli aminopeptidase P


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M35PDB ENTRY 1M35

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.225% PEG 4K, 0.1 MM EDTA, 0.1 M TRIS (PH 8.2), 0.2 M NA ACETATE CRYSTALS SOAKED IN 30% ISOPROPANOL PLUS 5 MM CACL2 FOR 10 MIN PRIOR TO FREEZING
Crystal Properties
Matthews coefficientSolvent content
4.471.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 208.359α = 90
b = 312.688β = 90
c = 160.198γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU RAXIS IICYALE MIRRORS1999-06-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200 H

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.43094.50.0419.62.1192310-340.59
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.48860.164.51.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1M352.4182.57182590968894.80.1760.1750.2RANDOM26.12
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]
-0.58-0.671.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.867
r_scangle_it3.097
r_scbond_it1.753
r_angle_refined_deg1.254
r_mcangle_it1.077
r_angle_other_deg0.833
r_mcbond_it0.529
r_symmetry_vdw_other0.295
r_nbd_other0.235
r_nbd_refined0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.867
r_scangle_it3.097
r_scbond_it1.753
r_angle_refined_deg1.254
r_mcangle_it1.077
r_angle_other_deg0.833
r_mcbond_it0.529
r_symmetry_vdw_other0.295
r_nbd_other0.235
r_nbd_refined0.2
r_symmetry_vdw_refined0.176
r_symmetry_hbond_refined0.156
r_xyhbond_nbd_refined0.15
r_nbtor_other0.086
r_chiral_restr0.073
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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 AtomsNumber
Protein Atoms20931
Nucleic Acid Atoms
Solvent Atoms1072
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling