X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5
Temperature 293.0
Details 20.00% polyethylene glycol 6000, 0.1M sodium citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 161.91 α = 90
b = 49.37 β = 114.45
c = 71.36 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
CCD MARMOSAIC 325 mm CCD Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) 2011-05-25
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 0.91837,0.97941,0.97904 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
1.25 28.5 97.3 0.041 -- -- -- -- 140636 -- -3.0 11.346
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)
1.25 1.29 97.4 0.501 -- 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 1.25 28.498 -- 0.0 -- 140635 7057 99.13 -- 0.1521 0.1508 0.1764 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 1.25 1.282 -- 514 9870 0.223 0.273 -- 99.79
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.7021
Anisotropic B[1][1] 0.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.1
Anisotropic B[2][2] -0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.14
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.466
r_dihedral_angle_2_deg 35.297
r_dihedral_angle_3_deg 11.527
r_mcbond_it 2.296
r_chiral_restr 0.097
r_gen_planes_other 0.001
r_scbond_it 4.012
r_sphericity_bonded 4.027
r_rigid_bond_restr 1.706
r_bond_other_d 0.001
r_mcbond_other 1.569
r_dihedral_angle_1_deg 6.122
r_dihedral_angle_4_deg 11.508
r_mcangle_it 3.083
r_gen_planes_refined 0.008
r_bond_refined_d 0.014
r_angle_other_deg 0.95
r_scangle_it 5.338
r_sphericity_free 6.546
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4031
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 550

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: December 6, 2010
REFMAC refinement version: 5.5.0110
XDS data reduction
SHELXD phasing