X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9.5
Temperature 277.0
Details 1.0000M NaCitrate, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.45 α = 90
b = 118.25 β = 90
c = 129.19 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 2009-07-30
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97925,0.97911 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
2.05 29.96 99.8 0.143 0.143 -- 3.7 -- 79699 -- -- 24.029
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)
2.05 2.1 100.0 0.804 0.804 1.6 3.7 5863

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 2.05 29.961 -- 0.0 -- 79629 3987 99.71 -- 0.187 0.184 0.24 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 2.05 2.103 -- 317 5514 0.26 0.332 -- 99.73
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.05
Anisotropic B[1][1] 0.69
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.35
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 0.58
r_mcbond_it 2.022
r_mcangle_it 3.216
r_angle_other_deg 0.924
r_gen_planes_refined 0.007
r_bond_other_d 0.001
r_chiral_restr 0.096
r_scangle_it 7.051
r_gen_planes_other 0.002
r_angle_refined_deg 1.583
r_dihedral_angle_4_deg 17.972
r_scbond_it 5.361
r_dihedral_angle_3_deg 14.245
r_bond_refined_d 0.017
r_dihedral_angle_1_deg 6.957
r_dihedral_angle_2_deg 36.278
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8777
Nucleic Acid Atoms 0
Heterogen Atoms 95
Solvent Atoms 785

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
PHENIX refinement
REFMAC refinement version: 5.5.0110
SCALA data scaling version: 3.2.5
PDB_EXTRACT data extraction version: 3.006
MOSFLM data reduction
HELXD phasing
autoSHARP phasing