5O27

Crystal structure of murine neuroglobin mutant V140W under 30 bar xenon pressure


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q1F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52931.6 M ammonium sulfate, 0.1 M MES, 10 % dioxane
Crystal Properties
Matthews coefficientSolvent content
2.6553.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.811α = 90
b = 89.811β = 90
c = 114.333γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDADSC QUANTUM 210rmirrors2011-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM160.980ESRFBM16

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
12.30864.30999.60.0860.0960.04112.94.9796128.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.312.4399.60.5760.5760.6410.2741.34.9

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 REPLACEMENTTHROUGHOUT1q1f2.3120754240199.320.15380.1510.2041RANDOM45.178
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]
-0.19-0.09-0.190.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.406
r_dihedral_angle_3_deg18.55
r_dihedral_angle_4_deg16.717
r_dihedral_angle_1_deg7.021
r_angle_refined_deg2.261
r_angle_other_deg1.231
r_chiral_restr0.145
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_gen_planes_other0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.406
r_dihedral_angle_3_deg18.55
r_dihedral_angle_4_deg16.717
r_dihedral_angle_1_deg7.021
r_angle_refined_deg2.261
r_angle_other_deg1.231
r_chiral_restr0.145
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_gen_planes_other0.005
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1179
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms56

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing