X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Small Tubes
pH 6.7
Temperature 289.0
Details 20 mg/mL protein in a buffer consisting of 10 mM BES, 0.5 mM EDTA, 3 mM DTT. T-state GPb crystals soaked with 20 mM inhibitor for 6 hrs, pH 6.7, SMALL TUBES, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.7 α = 90
b = 128.7 β = 90
c = 116.44 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2005-05-24
Diffraction Radiation
Monochromator Protocol
Crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX10.1 1.488 SRS PX10.1

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
1.97 30 93.9 0.065 -- -- 3.7 64845 64845 0.0 -3.0 26.5
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)
1.969 2.0 90.0 0.298 -- 4.2 3.8 3109

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
FOURIER SYNTHESIS 1.969 30.0 -- -- 61530 61530 3267 93.2 -- 0.19194 0.19082 0.21271 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 1.969 2.02 3267 222 4370 0.234 0.257 -- 90.59
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 27.836
Anisotropic B[1][1] 0.76
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.52
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.003
r_dihedral_angle_4_deg 19.753
r_bond_refined_d 0.007
r_scangle_it 1.905
r_dihedral_angle_2_deg 33.647
r_dihedral_angle_3_deg 14.864
r_chiral_restr 0.074
r_scbond_it 1.202
r_xyhbond_nbd_refined 0.093
r_symmetry_hbond_refined 0.069
r_symmetry_vdw_refined 0.143
r_angle_refined_deg 1.022
r_nbtor_refined 0.302
r_nbd_refined 0.181
r_mcangle_it 0.888
r_mcbond_it 0.521
r_dihedral_angle_1_deg 5.03
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6604
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 335

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
CNS refinement
HKL-2000 data collection
DENZO data reduction
SCALEPACK data scaling
CNS phasing