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_angle_refined_deg 4.056
r_chiral_restr 0.128
r_symmetry_vdw_refined 0.459
r_nbtor_refined 0.345
r_symmetry_hbond_refined 0.688
r_gen_planes_refined 0.017
r_nbd_refined 0.227
r_xyhbond_nbd_refined 0.451
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

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