2V1G

Crystal structure of radiation-induced myoglobin compound II - intermediate H at pH 5.2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WLAPDB ENTRY 1WLA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.26-10 MG/ML PROTEIN, 3.0 M AMMONIUM SULPHATE, 10.8% GLYCEROL PH 5.2, RT.
Crystal Properties
Matthews coefficientSolvent content
1.4431.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.862α = 90
b = 28.65β = 105.93
c = 35.352γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2000-02-15MSINGLE 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
11.352198.40.08224.226717
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)
11.351.3885.40.32.72.4

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 1WLA1.3520.812424812771000.1410.1390.174RANDOM13.23
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]
0.20.70.140.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.545
r_dihedral_angle_4_deg16.621
r_dihedral_angle_3_deg11.396
r_dihedral_angle_1_deg4.118
r_scangle_it3.31
r_scbond_it2.307
r_mcangle_it1.45
r_angle_refined_deg1.066
r_mcbond_it0.953
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.545
r_dihedral_angle_4_deg16.621
r_dihedral_angle_3_deg11.396
r_dihedral_angle_1_deg4.118
r_scangle_it3.31
r_scbond_it2.307
r_mcangle_it1.45
r_angle_refined_deg1.066
r_mcbond_it0.953
r_nbtor_refined0.323
r_symmetry_hbond_refined0.237
r_nbd_refined0.227
r_xyhbond_nbd_refined0.222
r_symmetry_vdw_refined0.214
r_chiral_restr0.072
r_bond_refined_d0.052
r_gen_planes_refined0.005
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 Atoms190
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling