X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.99
Temperature 293.0
Details 50mM Sodium Cacodylate, 1mM MnCl2, 1mM Spermine, 50% Methyl pentane diol, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 17.83 α = 90
b = 30.91 β = 90
c = 44.73 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2008-09-09
Diffraction Radiation
Monochromator Protocol
mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.54 -- --

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 15 95.2 0.105 0.0896 -- 4.56 1914 1819 -- -- 27.1
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)
2.0 2.07 99.4 0.2886 0.258 1.2 4.69 172

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 2.0 15.0 -- -- 1711 1711 77 96.08 -- 0.23892 0.23882 0.24078 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 2.0 2.051 123 4 123 0.329 0.105 -- 99.22
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 12.664
Anisotropic B[1][1] -0.7
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.57
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.27
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.116
r_gen_planes_refined 0.016
r_nbd_refined 0.182
r_nbtor_refined 0.303
r_bond_refined_d 0.027
r_symmetry_hbond_refined 0.113
r_symmetry_vdw_refined 0.183
r_chiral_restr 0.177
r_angle_refined_deg 3.767
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 240
Heterogen Atoms 0
Solvent Atoms 24

Software

Software
Software Name Purpose
MAR345 data collection
AMoRE phasing
REFMAC refinement version: 5.2.0019
AUTOMAR data reduction
SCALEPACK data scaling