X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 5
Temperature 293.0
Details 2.4 M Ammonium Sulfate; 0.1 M Citric Acid pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Method Vapor Diffusion Sitting Drop Nanodrop
pH 9
Temperature 293.0
Details 2.4 M Ammonium Sulfate; 0.1 M Bicine pH 9.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 92.36 α = 90
b = 92.36 β = 90
c = 135.83 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD APS-1 Flat mirror,single crystal Si(311) bent monochromator 2002-10-26
CCD ADSC QUANTUM 315 -- 2002-11-24
Diffraction Radiation
Monochromator Protocol
-- MAD
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.979, 0.991 APS 19-BM
SYNCHROTRON SSRL BEAMLINE BL11-1 -- 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
1.7 39.4 94.9 -- 0.086 -- 8.2 36314 36314 -- -- --
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 1.79 72.8 -- 0.643 1.7 3.4 3969

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 1.7 39.4 -- -- -- 34513 1800 94.79 -- 0.14651 0.14516 0.17242 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 -- 86 1755 0.285 0.305 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 13.858
Anisotropic B[1][1] 1.23
Anisotropic B[1][2] 0.62
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.85
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.812
r_scbond_it 5.087
r_symmetry_vdw_other 0.325
r_dihedral_angle_1_deg 5.802
r_symmetry_hbond_refined 0.295
r_mcbond_it 1.187
r_angle_refined_deg 1.522
r_nbtor_other 0.082
r_chiral_restr 0.096
r_symmetry_vdw_refined 0.149
r_bond_refined_d 0.016
r_gen_planes_refined 0.008
r_bond_other_d 0.002
r_gen_planes_other 0.008
r_scangle_it 7.91
r_nbd_refined 0.21
r_nbd_other 0.252
r_mcangle_it 2.176
r_xyhbond_nbd_refined 0.219
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1922
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 358

Software

Software
Software Name Purpose
MOSFLM data reduction
CCP4/SCALA data reduction
RESOLVE/SOLVE model building
XFIT/CCP4/TLS/REFMAC(5.1.24) refinement
CCP4 data scaling version: (SCALA)
RESOLVE/SOLVE phasing
REFMAC refinement version: 5.1.24