5LMM

Structure of E coli Hydrogenase Hyd-1 mutant E28Q


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 293.0
Details 100 mM tris pH 8.1 150 mM NaCl 200 mM LiSO4 20-24% PEG 3350

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.98 α = 90
b = 97.8 β = 90
c = 183.47 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M mirrors 2016-04-24
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03

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
1.2 91.74 97.9 0.14 -- -- 10.9 -- 511277 -- -- --
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)
1.2 1.22 95.6 1.964 -- 1.3 10.4 --

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 1.2 91.74 -- -- -- 485082 25987 97.72 -- 0.11893 0.11752 0.14561 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 1.2 1.231 -- 1808 34908 0.239 0.251 -- 95.59
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.04
Anisotropic B[1][1] 0.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.31
RMS Deviations
Key Refinement Restraint Deviation
r_bond_other_d 0.002
r_dihedral_angle_2_deg 34.901
r_gen_planes_other 0.002
r_scbond_it 2.407
r_dihedral_angle_3_deg 11.507
r_sphericity_bonded 7.433
r_long_range_B_refined 2.867
r_sphericity_free 21.839
r_angle_other_deg 1.112
r_mcbond_it 1.212
r_scbond_other 2.407
r_angle_refined_deg 1.785
r_gen_planes_refined 0.011
r_bond_refined_d 0.017
r_long_range_B_other 2.867
r_dihedral_angle_1_deg 6.023
r_rigid_bond_restr 2.765
r_chiral_restr 0.123
r_mcangle_other 1.43
r_dihedral_angle_4_deg 16.87
r_mcangle_it 1.43
r_scangle_other 2.755
r_mcbond_other 1.212
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13167
Nucleic Acid Atoms 0
Heterogen Atoms 123
Solvent Atoms 1426

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0155
DIALS data reduction
Aimless data scaling
PHASER phasing

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