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 cacoldylate, 10mM Barium chloride, 0.5mM Spermine, 30% (v/v) Methyl pentane diol , pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 17.54 α = 90
b = 30.51 β = 90
c = 44.21 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
IMAGE PLATE MARRESEARCH mirrors 2008-09-17
Diffraction Radiation
Monochromator Protocol
mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS MICROSTAR 1.5418 -- --

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
1.67 30 91.9 0.0882 0.0635 -- 4.54 3037 2791 -- -- 26.6
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)
1.67 1.73 89.6 0.2711 0.233 1.7 4.37 183

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 1.67 13.74 -- -- 2427 2427 145 86.05 -- 0.2173 0.21689 0.22312 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 1.673 1.716 12 12 183 0.32 0.245 -- 94.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 16.177
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] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.257
r_symmetry_hbond_refined 0.214
r_angle_refined_deg 2.247
r_gen_planes_refined 0.011
r_nbd_refined 0.212
r_scangle_it 2.583
r_metal_ion_refined 0.4
r_scbond_it 1.925
r_nbtor_refined 0.274
r_symmetry_vdw_refined 0.167
r_bond_refined_d 0.016
r_chiral_restr 0.094
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.224
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 249
Heterogen Atoms 2
Solvent Atoms 39

Software

Software
Software Name Purpose
MAR345dtb data collection
PHASER phasing
REFMAC refinement version: 5.2.0019
AUTOMAR data reduction
SCALEPACK data scaling