X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Evaporation
pH 6.5
Temperature 277.15
Details 12%MPD 0.1M MES-KOH pH6.5 50mM KCL 10mM NH4-CL 15mM Mg2CL, EVAPORATION, temperature 277.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 401 α = 90
b = 401 β = 90
c = 176 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-08-02
Diffraction Radiation
Monochromator Protocol
LENSES SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 1.000 DIAMOND I04

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
3.1 45.8 99.2 -- -- -- -- 241499 241499 1.0 1.0 --
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)
3.1 3.3 98.7 -- 0.632 1.8 2.9 --

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 3.162 29.88 -- -- 241499 219586 11558 95.44 -- 0.20002 0.19744 0.24905 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 3.162 3.243 -- 727 13501 0.313 0.345 -- 81.03
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 85.521
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.02
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 5.988
r_mcangle_it 10.453
r_mcbond_other 6.539
r_mcbond_it 6.539
r_gen_planes_other 0.001
r_gen_planes_refined 0.008
r_chiral_restr 0.104
r_dihedral_angle_4_deg 18.259
r_dihedral_angle_3_deg 23.62
r_dihedral_angle_2_deg 34.47
r_dihedral_angle_1_deg 9.011
r_angle_other_deg 1.276
r_angle_refined_deg 1.698
r_bond_other_d 0.002
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19120
Nucleic Acid Atoms 32785
Heterogen Atoms 18
Solvent Atoms 0

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.8.0016 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.8.0016 refinement