X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.8
Details CRYSTALS WERE GROWN IN DROPS CONTAINING 0.3 MM WILD-TYPE RK, 5 MM D-RIBOSE, 10 MM AMP-PCP, 75 MM MGCL2, 60 MM CSCL, 10% 2-METHYL-2,4-PENTANEDIOL, 10% POLYETHYLENE GLYCOL 4000 AND 50 MM SODIUM ACETATE, PH 4.8.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.45 α = 90
b = 62.77 β = 90
c = 339.28 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 MARRESEARCH -- 2000-02-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 -- ESRF ID14-1

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
2.34 17 98.2 0.091 -- -- 4.9 -- 50296 -- -- --
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)
2.34 2.38 99.9 0.377 -- 3.8 -- --

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
OTHER 2.34 17.0 -- -- -- 50296 2480 98.2 -- 0.196 0.193 0.257 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 2.34 2.4 -- 191 3481 0.207 0.296 -- --
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 8.007
r_scbond_it 5.394
r_mcangle_it 3.154
r_mcbond_it 1.924
r_nbd_refined 0.268
r_gen_planes_refined 0.005
r_chiral_restr 0.114
r_angle_other_deg 1.574
r_bond_refined_d 0.01
r_xyhbond_nbd_refined 0.157
r_metal_ion_refined 0.148
r_symmetry_vdw_refined 0.254
r_symmetry_hbond_refined 0.16
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8976
Nucleic Acid Atoms 0
Heterogen Atoms 137
Solvent Atoms 242

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC 5.0 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement