X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 0.95-1.0M citrate trisodium dihydrate, 100mM Hepes, 5mM deoxycytidine, 5mM ADP, 5mM MgCl2, 5mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80 α = 90
b = 80 β = 90
c = 93.95 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 -- 2001-03-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-D 0.9552 APS 14-BM-D

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
2.2 30 -- -- 0.064 -- -- -- 15208 -- -- --
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)
2.2 2.3 -- -- 0.156 7.5 -- --

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 2.21 20.0 -- 0.0 -- 13671 1537 95.79 -- 0.22733 0.22158 0.27964 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 2.209 2.266 -- 100 878 0.652 0.666 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 39.706
Anisotropic B[1][1] 2.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.34
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.095
r_nbd_other 0.25
r_nbd_refined 0.219
r_gen_planes_other 0.007
r_gen_planes_refined 0.008
r_chiral_restr 0.097
r_dihedral_angle_1_deg 7.942
r_angle_other_deg 0.915
r_angle_refined_deg 1.885
r_bond_other_d 0.002
r_bond_refined_d 0.021
r_xyhbond_nbd_refined 0.194
r_symmetry_vdw_refined 0.279
r_symmetry_vdw_other 0.3
r_symmetry_hbond_refined 0.395
r_mcbond_it 1.097
r_mcangle_it 2.0
r_scbond_it 2.658
r_scangle_it 4.25
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1869
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 131

Software

Computing
Computing Package Purpose
REFMAC 5.1.24 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.24 refinement