X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 293.0
Details 0.05M calcium acetate, 40% 1,2-propanediol, 0.1M sodium acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.77 α = 90
b = 86.77 β = 90
c = 85.63 γ = 90
Symmetry
Space Group I 4

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) 2013-03-21
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 0.97926,0.91837 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
1.7 27.44 97.6 0.046 -- -- -- -- 34782 -- -3.0 25.537
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)
1.7 1.76 93.2 0.788 -- 1.5 -- --

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 1.7 27.44 -- 0.0 -- 34780 1745 99.7 -- 0.1909 0.1897 0.212 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 1.7 1.744 -- 129 2397 0.293 0.321 -- 99.18
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.9645
Anisotropic B[1][1] 1.55
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.09
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 14.433
r_mcbond_other 2.393
r_dihedral_angle_1_deg 6.375
r_dihedral_angle_2_deg 39.971
r_gen_planes_refined 0.007
r_chiral_restr 0.086
r_bond_other_d 0.004
r_mcangle_it 3.889
r_gen_planes_other 0.004
r_bond_refined_d 0.01
r_mcbond_it 2.393
r_angle_refined_deg 1.392
r_dihedral_angle_4_deg 11.117
r_angle_other_deg 1.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2220
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 260

Software

Software
Software Name Purpose
MolProbity model building 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