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, 0.075M magnesium chloride, 0.1M KCL, pH 6.5, EVAPORATION, temperature 277.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 402.32 α = 90
b = 402.32 β = 90
c = 174.93 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2012-08-02
Diffraction Radiation
Monochromator Protocol
MIRRORS 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 48.93 98.95 -- -- -- -- 242068 254809 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)
3.098 3.178 98.33 -- -- -- -- --

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 3.098 48.93 -- 0.0 254809 254809 12741 98.95 0.1853 0.1853 0.1829 0.2318 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 3.098 3.178 -- 927 17610 0.307 0.335 -- 98.33
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 83.7225
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 6.68
r_mcangle_it 10.964
r_mcbond_it 6.927
r_gen_planes_refined 0.008
r_chiral_restr 0.121
r_dihedral_angle_4_deg 19.538
r_dihedral_angle_3_deg 24.456
r_dihedral_angle_2_deg 34.992
r_dihedral_angle_1_deg 8.494
r_angle_refined_deg 1.748
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19120
Nucleic Acid Atoms 32911
Heterogen Atoms 56
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 5.8.0021 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.8.0021 refinement