3EDB

Carbonmonoxy Sperm Whale Myoglobin at 120 K: Laser on [150 min]


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MBCPDB ENTRY 1MBC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1batch62932.4M Ammonium sulfate, 10mM TrisHCl, 100mM Sodium phosphate, pH 6.0, batch, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8934.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.434α = 90
b = 30.723β = 105.55
c = 63.865γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDMAR CCD 165 mm2007-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW14A0.827Photon FactoryAR-NW14A

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
11.215097.90.05612.93.638772-3
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)
1.211.2584.70.2782.93307

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 1MBC1.2115.6738755194698.390.1440.1420.182RANDOM14.744
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]
0.02-0.010.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.801
r_dihedral_angle_4_deg17.723
r_dihedral_angle_3_deg13.901
r_sphericity_free9.553
r_scangle_it5.778
r_sphericity_bonded5.45
r_dihedral_angle_1_deg4.857
r_scbond_it4.334
r_mcangle_it2.931
r_rigid_bond_restr2.829
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.801
r_dihedral_angle_4_deg17.723
r_dihedral_angle_3_deg13.901
r_sphericity_free9.553
r_scangle_it5.778
r_sphericity_bonded5.45
r_dihedral_angle_1_deg4.857
r_scbond_it4.334
r_mcangle_it2.931
r_rigid_bond_restr2.829
r_mcbond_it2.029
r_angle_refined_deg1.877
r_metal_ion_refined0.569
r_nbtor_refined0.32
r_nbd_refined0.307
r_symmetry_vdw_refined0.152
r_chiral_restr0.144
r_symmetry_hbond_refined0.142
r_xyhbond_nbd_refined0.106
r_bond_refined_d0.019
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1217
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms55

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling