X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 9
Details 0.1 M BICINE PH 9 AND 10% PEG 5K MME PROTEIN:RNA RATIO 4:1.2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 82.95 α = 90
b = 86.46 β = 106.63
c = 90.19 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD (MAR225) MARRESEARCH -- 2012-11-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 -- ESRF ID23-2

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
3.4 50 99.6 0.18 -- -- 3.4 -- 18433 -- 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)
3.4 3.5 99.6 0.79 -- 1.89 3.4 --

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 3.4 44.35 -- -- -- 16130 867 99.7 -- 0.20098 0.19827 0.25213 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 3.4 3.488 -- 63 1197 0.324 0.373 -- 99.76
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 83.212
Anisotropic B[1][1] -8.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.55
Anisotropic B[2][2] -5.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.93
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.004
r_chiral_restr 0.067
r_dihedral_angle_4_deg 12.848
r_dihedral_angle_3_deg 16.572
r_dihedral_angle_2_deg 38.065
r_dihedral_angle_1_deg 6.386
r_angle_other_deg 0.864
r_angle_refined_deg 1.12
r_bond_other_d 0.004
r_bond_refined_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7282
Nucleic Acid Atoms 877
Heterogen Atoms 0
Solvent Atoms 0

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0029 refinement
PHASER model building