X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.5
Details MAGNESIUM CHLORIDE, DNA, DB 985, MPD, SODIUM CACODYLATE BUFFER. PH 6.6, VAPOUR DIFFUSION, SITTING DROP, 285K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 24.03 α = 90
b = 39.9 β = 90
c = 65.78 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC TOROIDAL MIRROR 2009-07-19
Diffraction Radiation
Monochromator Protocol
SI (111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 -- ESRF ID14-4

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
1.25 39.9 99.0 0.05 -- -- 6.5 -- 18006 -- 0.0 0.0
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)
1.25 1.32 100.0 0.55 -- 3.1 6.6 --

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
MOLECULAR REPLACEMENT 1.25 14.76 -- -- -- 17027 925 98.84 -- 0.15755 0.15483 0.20704 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 1.25 1.282 -- 82 1230 0.212 0.274 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 12.92
Anisotropic B[1][1] -0.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.12
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.25
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 7.302
r_rigid_bond_restr 2.644
r_scangle_it 4.309
r_scbond_it 3.329
r_gen_planes_other 0.037
r_gen_planes_refined 0.034
r_chiral_restr 0.111
r_angle_other_deg 4.559
r_angle_refined_deg 2.574
r_bond_other_d 0.001
r_bond_refined_d 0.02
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 486
Heterogen Atoms 31
Solvent Atoms 192

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0110 refinement
PHASER model building