5O18

Crystal structure of murine neuroglobin mutant V140W


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 1.6 M ammonium sulfate, 0.1 M MES, 10 % dioxane

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.56 α = 90
b = 88.56 β = 90
c = 116.21 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r mirrors 2011-02-20
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM16 0.980 ESRF BM16

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.86 23.16 97.5 -- 0.056 10.5 7.0 -- 14557 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.86 1.96 88.8 0.644 0.644 1.2 4.3 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.86 20.0 -- 0.0 -- 13852 699 96.94 -- 0.1808 0.179 0.2218 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.858 1.906 -- 61 768 0.303 0.34 0.0 77.26
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.665
Anisotropic B[1][1] -0.1
Anisotropic B[1][2] -0.05
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.1
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.31
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 31.247
r_bond_refined_d 0.02
r_gen_planes_refined 0.011
r_gen_planes_other 0.005
r_angle_other_deg 1.629
r_dihedral_angle_1_deg 5.876
r_angle_refined_deg 1.975
r_dihedral_angle_4_deg 14.695
r_dihedral_angle_3_deg 16.865
r_bond_other_d 0.002
r_chiral_restr 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1179
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 55

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0135
SCALA data scaling version: 6.1
PDB_EXTRACT data extraction version: 3.22
XDS data reduction
PHASER phasing version: 2.3.0