X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 6
Temperature 277.0
Details 30% MPD, MES buffer pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.71 α = 90
b = 63.71 β = 90
c = 78.04 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 flat mirror 2003-04-17
Diffraction Radiation
Monochromator Protocol
single crystal Si(111) bent monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.98397, 0.97922, 0.91837, 0.97855 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
1.9 31.86 99.9 -- 0.05 -- 8.8 14860 14860 -- -- 48.07
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 99.9 -- 0.638 2.3 4.9 1058

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 31.86 -- -- -- 14131 728 99.87 -- 0.19059 0.18843 0.23508 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 -- 63 1002 0.284 0.319 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 41.843
Anisotropic B[1][1] 1.05
Anisotropic B[1][2] 0.52
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.57
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.391
r_scbond_it 2.797
r_mcangle_it 1.454
r_mcbond_it 0.768
r_symmetry_hbond_refined 0.118
r_symmetry_vdw_other 0.213
r_symmetry_vdw_refined 0.199
r_xyhbond_nbd_refined 0.146
r_nbtor_other 0.081
r_nbd_other 0.158
r_bond_refined_d 0.018
r_bond_other_d 0.001
r_angle_refined_deg 1.225
r_angle_other_deg 0.758
r_dihedral_angle_1_deg 5.088
r_dihedral_angle_2_deg 36.23
r_dihedral_angle_3_deg 13.39
r_dihedral_angle_4_deg 15.595
r_chiral_restr 0.076
r_gen_planes_refined 0.004
r_gen_planes_other 0.001
r_nbd_refined 0.207
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 974
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 90

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SOLVE/RESOLVE Structure Solution
REFMAC 5.1.9999 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.9999 refinement
RESOLVE model building
SOLVE model building
SCALA(CCP4 version: 4.2) data reduction
MOSFLM data collection