X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 277.0
Details NANODROP, 1.0M LiCl, 20.0% PEG 6000, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.83 α = 90
b = 67.23 β = 90
c = 131.4 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 Flat collimating mirror, toroid focusing mirror 2008-01-13
Diffraction Radiation
Monochromator Protocol
Double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162, 0.97980, 0.97968 SSRL BL9-2

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
1.9 29.92 99.2 0.056 -- -- -- -- 40355 -- -3.0 27.041
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)
1.9 1.97 95.6 0.502 -- 1.7 -- --

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 1.9 29.921 -- 0.0 -- 40297 2024 99.38 -- 0.182 0.18 0.219 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 1.9 1.948 -- 137 2668 0.271 0.355 -- 94.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.054
Anisotropic B[1][1] 0.93
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.46
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 17.483
r_dihedral_angle_1_deg 4.164
r_bond_refined_d 0.017
r_scangle_it 8.654
r_dihedral_angle_3_deg 12.57
r_chiral_restr 0.106
r_bond_other_d 0.002
r_mcbond_it 2.034
r_angle_refined_deg 1.704
r_gen_planes_refined 0.008
r_scbond_it 5.949
r_gen_planes_other 0.003
r_mcbond_other 0.595
r_mcangle_it 3.455
r_dihedral_angle_2_deg 33.601
r_angle_other_deg 1.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3754
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 393

Software

Software
Software Name Purpose
REFMAC refinement version: 5.4.0067
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.000
MAR345 data collection version: CCD
XDS data reduction
SHELXD phasing
autoSHARP phasing