X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 289.0
Details 0.1 M SPG buffer, 25% w/v PEG 1500, 10 uM Spermidine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.49 α = 90
b = 147.1 β = 93.68
c = 47.78 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2009-11-11
Diffraction Radiation
Monochromator Protocol
Double crystal, Si(111) or Si(311) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9395 ESRF ID14-4

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
2.7 73.55 98.9 -- 0.066 -- 3.4 17783 17783 -- -- --
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)
2.7 2.85 99.7 0.201 0.201 3.8 3.5 2610

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 2.8 45.36 -- 0.0 22705 15885 791 98.71 -- 0.2072 0.2057 0.2367 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 2.8 2.873 -- 42 1106 0.265 0.355 -- 99.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.88
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] -0.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.13
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 4.714
r_mcbond_it 0.359
r_mcangle_it 0.719
r_bond_refined_d 0.009
r_dihedral_angle_3_deg 16.973
r_dihedral_angle_4_deg 25.046
r_angle_refined_deg 1.52
r_dihedral_angle_2_deg 28.486
r_scbond_it 1.146
r_scangle_it 1.897
r_chiral_restr 0.067
r_gen_planes_refined 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2479
Nucleic Acid Atoms 1546
Heterogen Atoms 1
Solvent Atoms 13

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.3.9
PHASER phasing version: 2.1.4
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
MxCuBE data collection