X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Temperature 298.0
Details Buffer conditions: 25 mM K-HEPES (pH 7.5), 12.5 mM Na-cacodylate pH 5.5, 2.5 mM Tris-HCl (pH 7.5), 80 mM NH_4 Cl, 80 mM KCl, 11 mM MgCl_2, 6.5 mM Thermine HCl and 0.2 M KSCN. Crystallization by the hanging drop method over 26-30% MPD in the above buffer mix, using 2 uL of ribosome complex mixed with 2 uL of well mixture on siliconized cover slips, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 507.21 α = 90
b = 507.21 β = 90
c = 692.51 γ = 90
Symmetry
Space Group I 4 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2004-07-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 12.3.1 0.9835 ALS 12.3.1

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
3.83 78 82.0 0.15 -- -- -- -- 354761 0.0 0.0 --

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
-- 3.83 30.0 -- 0.0 -- 346189 10068 81.68 -- 0.327 0.327 0.351 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 3.83 3.928 -- 310 9243 0.387 0.385 -- 31.13
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 0.0
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.09
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 0.0
r_nbtor_refined 0.302
r_scbond_it 0.0
r_gen_planes_refined 0.011
r_dihedral_angle_3_deg 18.93
r_nbd_refined 0.316
r_dihedral_angle_1_deg 3.429
r_bond_refined_d 0.009
r_mcangle_it 0.0
r_mcbond_it 0.0
r_dihedral_angle_4_deg 15.665
r_chiral_restr 0.082
r_symmetry_vdw_refined 0.41
r_dihedral_angle_2_deg 40.383
r_xyhbond_nbd_refined 0.227
r_symmetry_hbond_refined 0.277
r_angle_refined_deg 1.237
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 26862
Nucleic Acid Atoms 64786
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.000
ADSC data collection version: Quantum
CNS refinement
d*TREK data reduction
SCALA data scaling
CNS phasing