X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6.5
Temperature 277.15
Details 01.M MES-KOH, 50mM KCL, 15mM Mg+2-acetate, 12% MPD, pH 6.5, VAPOR DIFFUSION, temperature 277.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 401.3 α = 90
b = 401.3 β = 90
c = 173.68 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- --
Diffraction Radiation
Monochromator Protocol
-- 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
3.4 20 98.12 -- -- -- -- -- 189418 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)
3.4 3.486 99.94 -- -- -- -- --

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 3.4 20.0 -- -- -- 179946 9471 98.12 -- 0.19 0.18729 0.24184 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 3.4 3.486 -- 686 13045 0.261 0.31 -- 99.94
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 90.683
Anisotropic B[1][1] -0.39
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.78
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 5.832
r_mcangle_it 9.967
r_mcbond_other 6.236
r_mcbond_it 6.236
r_gen_planes_other 0.002
r_gen_planes_refined 0.007
r_chiral_restr 0.095
r_dihedral_angle_4_deg 18.03
r_dihedral_angle_3_deg 22.097
r_dihedral_angle_2_deg 34.193
r_dihedral_angle_1_deg 7.493
r_angle_other_deg 1.25
r_angle_refined_deg 1.421
r_bond_other_d 0.004
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19130
Nucleic Acid Atoms 32785
Heterogen Atoms 0
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 5.8.0033 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.8.0033 refinement