X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details 0.2M magnesium acetate, 30.0% 2-methyl-2,4-pentanediol, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.65 α = 90
b = 59.32 β = 101.38
c = 58.41 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2014-05-21
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) bent MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.97939,0.91837,0.97882 SSRL BL11-1

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
2.56 42.84 97.5 0.102 -- -- -- -- 11309 -- -3.0 53.294
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)
2.56 2.65 97.5 0.652 -- 2.1 -- --

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
MAD 2.56 42.844 -- 0.0 -- 10762 543 97.77 -- 0.2551 0.2528 0.2989 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 2.56 2.626 -- 27 793 0.358 0.331 -- 98.68
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.3173
Anisotropic B[1][1] 1.64
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.95
Anisotropic B[2][2] -5.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.7
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.658
r_angle_refined_deg 1.483
r_gen_planes_refined 0.006
r_dihedral_angle_3_deg 15.548
r_dihedral_angle_4_deg 28.965
r_bond_refined_d 0.011
r_angle_other_deg 1.084
r_gen_planes_other 0.004
r_mcbond_other 1.656
r_mcangle_it 2.654
r_dihedral_angle_2_deg 40.455
r_bond_other_d 0.004
r_chiral_restr 0.08
r_mcbond_it 1.664
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2232
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 4

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling
REFMAC refinement version: 5.7.0032
XDS data reduction
SHELXD phasing