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 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 52.71 α = 90
b = 132.81 β = 90
c = 157.57 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2001-12-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-D 0.9000 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
1.96 30 -- -- 0.045 -- 6.9 -- 39365 -- -- 25.0
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)
1.96 2.0 -- -- 0.291 3.3 -- --

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 1.96 30.0 -- -- -- 35428 3936 98.67 -- 0.16491 0.16066 0.2035 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 1.965 2.016 -- 245 2361 0.196 0.259 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.099
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.43
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.38
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.107
r_gen_planes_refined 0.01
r_scbond_it 2.893
r_angle_refined_deg 1.922
r_xyhbond_nbd_refined 0.191
r_bond_other_d 0.002
r_nbd_other 0.245
r_bond_refined_d 0.02
r_symmetry_vdw_refined 0.3
r_gen_planes_other 0.007
r_nbtor_other 0.089
r_symmetry_hbond_refined 0.401
r_angle_other_deg 1.254
r_mcangle_it 2.104
r_nbd_refined 0.216
r_dihedral_angle_1_deg 6.22
r_mcbond_it 1.158
r_scangle_it 4.522
r_symmetry_vdw_other 0.294
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3819
Nucleic Acid Atoms 0
Heterogen Atoms 86
Solvent Atoms 333

Software

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