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, 5mM MnCl2, 1mM Spermine, 50% methyl pentane diol, pH 6.99, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 17.88 α = 90
b = 30.97 β = 90
c = 43.4 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH mirrors 2008-11-20
Diffraction Radiation
Monochromator Protocol
mirror SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE BRUKER AXS MICROSTAR 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 15 98.8 0.041 0.0383 -- 3.83 751 742 -- -- 40.616
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)
2.15 2.23 100.0 0.2377 0.2162 2.0 3.87 82

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 2.15 14.7 -- -- 694 693 41 99.73 -- 0.2687 0.26859 0.27015 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 2.153 2.208 55 1 55 0.358 0.066 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 30.334
Anisotropic B[1][1] -1.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.45
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.57
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.688
r_symmetry_vdw_refined 0.459
r_xyhbond_nbd_refined 0.451
r_nbtor_refined 0.345
r_nbd_refined 0.227
r_gen_planes_refined 0.017
r_chiral_restr 0.128
r_angle_refined_deg 4.056
r_bond_refined_d 0.021
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 0
Nucleic Acid Atoms 121
Heterogen Atoms 4
Solvent Atoms 6

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
AUTOMAR Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMoRE Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
AMoRE model building
MAR345dtb data collection