1JP8

Sperm Whale met-Myoglobin (room temperature; high pressure)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VXHPDB ENTRY 1VXH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1batch6298ammonium sulfate, pH 6, batch, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.9135.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.09α = 90
b = 30.8β = 105.69
c = 34.57γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295AREA DETECTORUCSD MARK II1997-12-05MSINGLE WAVELENGTH
21x-ray295AREA DETECTORUCSD MARK II1998-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.541
2ROTATING ANODERIGAKU1.541

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
1,22.39.290.10.05712.12.95327532718.6
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)
2.32.4279.60.13862.4671

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUTPDB ENTRY 1VXH2.39.142530656090.70.1650.236RANDOM15.1
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]
-5.46-0.852.093.36
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d16.5
c_scangle_it3.36
c_scbond_it2.23
c_mcangle_it2.1
c_mcbond_it1.32
c_improper_angle_d1.02
c_angle_deg1
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d16.5
c_scangle_it3.36
c_scbond_it2.23
c_mcangle_it2.1
c_mcbond_it1.32
c_improper_angle_d1.02
c_angle_deg1
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1212
Nucleic Acid Atoms
Solvent Atoms66
Heterogen Atoms58

Software

Software
Software NamePurpose
CNSrefinement
CCP4data scaling
CNSphasing