5O1K

Crystal structure of murine neuroglobin mutant V140W under 20 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
2.6553.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.257α = 90
b = 89.257β = 90
c = 115.416γ = 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
12.04823.12199.60.0770.0920.03414.67.41132328.01
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)
12.052.1697.90.7580.7580.8820.32317.3

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 REPLACEMENTTHROUGHOUT1q1f2.05201075056599.480.15490.15240.2022RANDOM43.341
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]
0.10.050.1-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.08
r_dihedral_angle_4_deg15.977
r_dihedral_angle_3_deg15.714
r_dihedral_angle_1_deg6.107
r_angle_refined_deg2.035
r_angle_other_deg1.554
r_chiral_restr0.125
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_gen_planes_other0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.08
r_dihedral_angle_4_deg15.977
r_dihedral_angle_3_deg15.714
r_dihedral_angle_1_deg6.107
r_angle_refined_deg2.035
r_angle_other_deg1.554
r_chiral_restr0.125
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_gen_planes_other0.004
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1179
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms60

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing