X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 277.0
Details NANODROP, 20.0% PEG 6000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.9 α = 90
b = 75.9 β = 90
c = 323.39 γ = 120
Symmetry
Space Group P 61 2 2

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 2008-12-07
Diffraction Radiation
Monochromator Protocol
Double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162, 0.97982, 0.97966 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 29.4 100.0 0.143 0.143 -- 7.1 -- 44914 -- -- 18.609
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 1.95 100.0 0.778 0.778 1.0 7.2 3207

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 29.399 -- 0.0 -- 44778 2257 100.0 -- 0.17 0.168 0.209 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 1.949 -- 170 3023 0.226 0.324 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.717
Anisotropic B[1][1] 0.38
Anisotropic B[1][2] 0.19
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.57
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 11.594
r_nbd_refined 0.21
r_symmetry_hbond_refined 0.188
r_xyhbond_nbd_refined 0.197
r_nbtor_refined 0.187
r_bond_refined_d 0.013
r_mcangle_it 2.602
r_dihedral_angle_2_deg 30.751
r_nbtor_other 0.088
r_gen_planes_refined 0.006
r_chiral_restr 0.082
r_mcbond_other 0.453
r_angle_other_deg 1.025
r_angle_refined_deg 1.544
r_symmetry_vdw_refined 0.152
r_dihedral_angle_1_deg 4.004
r_scangle_it 4.814
r_gen_planes_other 0.002
r_symmetry_vdw_other 0.26
r_scbond_it 4.002
r_mcbond_it 1.861
r_bond_other_d 0.002
r_xyhbond_nbd_other 0.205
r_dihedral_angle_4_deg 9.954
r_nbd_other 0.178
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3106
Nucleic Acid Atoms 0
Heterogen Atoms 55
Solvent Atoms 471

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
MAR345 data collection version: CCD
MOSFLM data reduction
SHELXD phasing
autoSHARP phasing