2V1K

Crystal structure of ferrous deoxymyoglobin at pH 6.8


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GJNPDB ENTRY 1GJN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.8BATCH METHOD: 6-12 MG/ML MYOGLOBIN, 80-85% OF THE CRYSTALLIZATION STOCK-SOLUTION (3.9 M AMMONIUM SULPHATE, 0.1 M MOPS AND 5-10% OF GLYCEROL PH 6.8)
Crystal Properties
Matthews coefficientSolvent content
1.4615.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.9α = 90
b = 28.75β = 105.72
c = 35.44γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATEMARRESEARCH2004-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM1AESRFBM1A

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
11.2533.997.10.052.342.6233121
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)
11.251.3295.50.184.182.27

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 1GJN1.2526.7831498167597.20.1360.1340.164RANDOM16.38
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]
-0.290.030.120.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.122
r_dihedral_angle_4_deg17.419
r_dihedral_angle_3_deg11.406
r_dihedral_angle_1_deg4.112
r_scangle_it3.799
r_scbond_it2.818
r_mcangle_it2.796
r_mcbond_it2.096
r_angle_refined_deg0.979
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.122
r_dihedral_angle_4_deg17.419
r_dihedral_angle_3_deg11.406
r_dihedral_angle_1_deg4.112
r_scangle_it3.799
r_scbond_it2.818
r_mcangle_it2.796
r_mcbond_it2.096
r_angle_refined_deg0.979
r_nbtor_refined0.322
r_symmetry_vdw_refined0.224
r_nbd_refined0.221
r_symmetry_hbond_refined0.22
r_xyhbond_nbd_refined0.2
r_chiral_restr0.085
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms1199
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling