X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 298.0
Details 20%(w/v)PEG1K, 100mM magnesium acetate, 100mM TRIS, 5mM gemcitabine, 5mM ADP, 5mM MgCl2, 5mM DTT, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.2 α = 90
b = 81.2 β = 90
c = 94.6 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2002-11-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID

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 30 -- -- 0.054 -- 11.9 -- 25412 -- -- 30.2
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 -- -- 0.533 4.7 -- --

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 20.0 -- 0.0 -- 22863 2549 99.51 -- 0.18171 0.17892 0.20713 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 -- 191 1629 0.252 0.291 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.92
Anisotropic B[1][1] 1.46
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.92
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.13
r_nbd_other 0.244
r_angle_other_deg 0.954
r_scbond_it 3.089
r_scangle_it 4.879
r_bond_other_d 0.002
r_symmetry_vdw_other 0.32
r_gen_planes_other 0.013
r_mcangle_it 2.213
r_symmetry_hbond_refined 0.179
r_xyhbond_nbd_refined 0.142
r_gen_planes_refined 0.011
r_nbd_refined 0.216
r_nbtor_other 0.082
r_mcbond_it 1.26
r_bond_refined_d 0.021
r_angle_refined_deg 1.78
r_dihedral_angle_1_deg 5.912
r_chiral_restr 0.112
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1892
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 144

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
XDS data scaling
SOLVE phasing