5YKP

Human methionine aminopeptidase type 1b (F309M mutant) in complex with ovalicin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GZ5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62980.1M Hepes pH-6.0, 19% PEG MME 2000
Crystal Properties
Matthews coefficientSolvent content
2.5651.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.713α = 90
b = 77.398β = 91.62
c = 47.489γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2015-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.682799.90.070.0820.04313.33.639533
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.681.7499.20.5010.5990.3230.8143.2

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 REPLACEMENTTHROUGHOUT2GZ51.6823.7537665184099.180.17680.17510.2117RANDOM28.03
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]
1.91.93-2.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.95
r_dihedral_angle_4_deg16.142
r_dihedral_angle_3_deg13.733
r_dihedral_angle_1_deg6.89
r_angle_refined_deg1.665
r_angle_other_deg1.46
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.95
r_dihedral_angle_4_deg16.142
r_dihedral_angle_3_deg13.733
r_dihedral_angle_1_deg6.89
r_angle_refined_deg1.665
r_angle_other_deg1.46
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2400
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
Cootmodel building
PDB_EXTRACTdata extraction