X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Small Tubes
pH 6.7
Temperature 289.0
Details Crystals grown from 20 mg/ml of protein in a buffer solution containing 10 mM BES pH 6.7, 1 mM EDTA and 3 mM DTT. 20mM inhibitor in 20% DMSO soaked with T-state native enzyme crystal for 11.5 hrs, SMALL TUBES, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.84 α = 90
b = 128.84 β = 90
c = 116.32 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 273
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2008-07-14
Diffraction Radiation
Monochromator Protocol
Crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX10.1 0.979 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
1.95 30 99.5 0.077 -- -- 4.7 71273 71273 0.0 -3.0 --
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)
1.95 1.98 97.4 0.428 -- 3.14 3.0 --

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 1.95 29.53 -- -- 67586 67586 3611 99.49 -- 0.18268 0.18099 0.21477 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 1.95 2.001 -- 279 4788 0.251 0.286 -- 97.67
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 33.285
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.139
r_angle_refined_deg 1.155
r_mcbond_it 0.636
r_dihedral_angle_1_deg 5.333
r_dihedral_angle_3_deg 14.988
r_nbtor_refined 0.304
r_dihedral_angle_4_deg 18.097
r_gen_planes_refined 0.005
r_bond_refined_d 0.009
r_scangle_it 3.192
r_nbd_refined 0.183
r_dihedral_angle_2_deg 34.997
r_symmetry_hbond_refined 0.061
r_mcangle_it 1.234
r_scbond_it 1.851
r_xyhbond_nbd_refined 0.101
r_chiral_restr 0.086
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6597
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 290

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
CNS refinement
HKL-3000 data collection
DENZO data reduction
SCALEPACK data scaling
CNS phasing