6AMP

Crystal structure of H172A PHM (CuH absent, CuM present)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PHM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.529319-24% PEG 4000, Tris HCL, 0.54 M MgCl2
Crystal Properties
Matthews coefficientSolvent content
1.9837.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.422α = 90
b = 66.362β = 90
c = 69.79γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2014-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.5418

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
12.485099.10.06812.44.510124
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)
12.482.5295.50.3663.7

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 REPLACEMENTTHROUGHOUTpdbid XX2.4848.09958350798.940.2170.21320.2903RANDOM49.564
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]
-0.512.54-2.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.311
r_dihedral_angle_3_deg18.146
r_dihedral_angle_4_deg15.295
r_dihedral_angle_1_deg8.585
r_angle_refined_deg1.693
r_angle_other_deg1.016
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.311
r_dihedral_angle_3_deg18.146
r_dihedral_angle_4_deg15.295
r_dihedral_angle_1_deg8.585
r_angle_refined_deg1.693
r_angle_other_deg1.016
r_chiral_restr0.096
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2380
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
Cootmodel building
SCALEPACKdata reduction
REFMACphasing