X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 277.0
Details 30.0000% PEG-6000, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.53 α = 90
b = 58.53 β = 90
c = 94.12 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 2009-05-13
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 -- 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
1.7 29.26 99.4 0.098 0.098 -- 4.8 -- 30021 -- -- 18.456
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 1.74 96.1 0.66 0.66 1.2 4.4 2089

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
SAD 1.7 29.26 -- 0.0 -- 29976 1517 99.18 -- 0.166 0.164 0.192 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 -- 106 1979 0.226 0.271 -- 95.25
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 20.711
Anisotropic B[1][1] -0.61
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.32
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.93
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.465
r_nbtor_other 0.089
r_symmetry_vdw_other 0.258
r_mcbond_other 0.632
r_scangle_it 5.654
r_gen_planes_refined 0.007
r_gen_planes_other 0.002
r_dihedral_angle_4_deg 20.483
r_xyhbond_nbd_refined 0.171
r_symmetry_hbond_refined 0.165
r_dihedral_angle_2_deg 34.315
r_nbd_other 0.176
r_nbtor_refined 0.178
r_bond_other_d 0.004
r_mcangle_it 2.603
r_dihedral_angle_1_deg 4.945
r_mcbond_it 2.114
r_chiral_restr 0.086
r_nbd_refined 0.238
r_symmetry_vdw_refined 0.104
r_scbond_it 4.033
r_angle_other_deg 0.935
r_dihedral_angle_3_deg 13.687
r_bond_refined_d 0.017
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2029
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 341

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
SCALA data scaling version: 3.2.5
PDB_EXTRACT data extraction version: 3.006
MOSFLM data reduction
SHARP phasing