X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 277.0
Details 20.00% polyethylene glycol 6000, 0.1M sodium citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.7 α = 90
b = 55.14 β = 90
c = 84.6 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
CCD MARMOSAIC 325 mm CCD Vertical focusing mirror; double crystal Si(111) monochromator 2011-03-05
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL14-1 0.95369,0.97915 SSRL BL14-1

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
0.95 28.2 99.4 -- 0.063 -- 5.2 131023 131023 -- -- 6.707
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)
0.95 0.97 96.7 0.67 0.67 1.9 4.1 9292

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 0.95 28.2 -- 0.0 -- 130918 6590 99.2 -- 0.1197 0.1191 0.1315 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 0.95 0.975 -- 450 8765 0.311 0.322 -- 95.68
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.9317
Anisotropic B[1][1] -0.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.56
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.39
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.011
r_dihedral_angle_1_deg 5.777
r_dihedral_angle_3_deg 11.882
r_sphericity_free 9.303
r_mcangle_it 2.904
r_scbond_it 2.883
r_dihedral_angle_4_deg 8.95
r_dihedral_angle_2_deg 36.779
r_mcbond_other 1.107
r_chiral_restr 0.113
r_gen_planes_other 0.005
r_mcbond_it 1.997
r_scangle_it 4.07
r_sphericity_bonded 4.418
r_bond_refined_d 0.018
r_rigid_bond_restr 1.423
r_angle_other_deg 1.222
r_bond_other_d 0.002
r_angle_refined_deg 1.832
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1718
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 386

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PDB_EXTRACT data extraction version: 3.10
SHELX phasing
SHARP phasing
SCALA data scaling version: 3.3.15
REFMAC refinement version: 5.5.0110
MOSFLM data reduction
SHELXD phasing