5EV5

Crystal structure of murine neuroglobin mutant V101F at 150 MPa pressure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4O4T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52931.6 M ammonium sulfate, 0.1 M MES, 10 % dioxane
Crystal Properties
Matthews coefficientSolvent content
2.652.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.024α = 90
b = 89.024β = 90
c = 113.879γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMAR555 FLAT PANEL2013-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID090.4104ESRFID09

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.9543.96499.40.0890.1020.0510.24.1124331243326.06
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0699.70.7290.7290.410.74.21807

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 REPLACEMENTTHROUGHOUT4O4T2201055254292.540.15520.15290.2027RANDOM31.515
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]
0.120.060.12-0.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.107
r_dihedral_angle_4_deg18.08
r_dihedral_angle_3_deg14.763
r_dihedral_angle_1_deg5.729
r_mcangle_it4.435
r_mcbond_it2.983
r_mcbond_other2.956
r_angle_other_deg2.206
r_angle_refined_deg2
r_chiral_restr0.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.107
r_dihedral_angle_4_deg18.08
r_dihedral_angle_3_deg14.763
r_dihedral_angle_1_deg5.729
r_mcangle_it4.435
r_mcbond_it2.983
r_mcbond_other2.956
r_angle_other_deg2.206
r_angle_refined_deg2
r_chiral_restr0.148
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_gen_planes_other0.008
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1176
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
DMphasing
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling