X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 277.0
Details 0.1M bicine pH 9, 2.4M ammonium sulfate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 133.88 α = 90
b = 133.88 β = 90
c = 127.5 γ = 120
Symmetry
Space Group H 3 2

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) 2013-01-24
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 0.91837,0.97932 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
2.1 28.71 99.5 0.106 -- -- -- -- 25691 -- -3.0 33.623
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)
2.1 2.17 99.0 0.862 -- 1.6 -- --

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 2.1 28.711 -- 0.0 -- 25691 1307 99.73 -- 0.1731 0.1707 0.2202 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 2.1 2.155 -- 86 1789 0.233 0.289 -- 99.26
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.5498
Anisotropic B[1][1] 0.65
Anisotropic B[1][2] 0.65
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.65
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.1
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 3.93
r_angle_refined_deg 1.782
r_chiral_restr 0.106
r_angle_other_deg 0.803
r_dihedral_angle_1_deg 3.099
r_dihedral_angle_4_deg 10.66
r_dihedral_angle_3_deg 10.337
r_bond_refined_d 0.011
r_dihedral_angle_2_deg 31.971
r_gen_planes_other 0.001
r_mcbond_other 3.924
r_mcangle_it 5.07
r_bond_other_d 0.001
r_gen_planes_refined 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2717
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 166

Software

Software
Software Name Purpose
MOLPROBITY validation version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
XSCALE data scaling version: July 4, 2012
REFMAC refinement version: 5.7.0032
XDS data reduction
SHELXD phasing
autoSHARP phasing