X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details PEG 8000, sodium HEPES, manganese chloride glycerol, hexanediol, 3'-deoxy-ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.69 α = 90
b = 119.85 β = 90
c = 159.5 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 105
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Osmic mirrors 2001-06-14
Diffraction Radiation
Monochromator Protocol
Osmic mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.5418 -- --

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
2.7 40 99.9 0.097 0.097 -- 5.8 37963 37963 -3.0 -3.0 69.0
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)
2.7 2.8 100.0 0.722 0.722 2.4 5.5 3733

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 2.7 31.16 0.0 0.0 38016 34165 3795 100.0 0.241 0.24081 0.23789 0.26747 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 2.7 2.77 2765 281 -- 0.288 0.318 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 28.407
Anisotropic B[1][1] 1.5
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.57
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.623
r_dihedral_angle_3_deg 20.422
r_chiral_restr 0.099
r_scangle_it 4.119
r_mcbond_it 1.116
r_symmetry_hbond_refined 0.151
r_symmetry_vdw_refined 0.128
r_gen_planes_refined 0.005
r_angle_refined_deg 1.426
r_xyhbond_nbd_refined 0.144
r_nbd_refined 0.166
r_mcangle_it 1.905
r_dihedral_angle_1_deg 3.161
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7776
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 44

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
REFMAC refinement version: 5.0
CNS phasing