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_gen_planes_other 0.002
r_angle_refined_deg 1.421
r_bond_other_d 0.004
r_dihedral_angle_3_deg 22.097
r_dihedral_angle_1_deg 7.493
r_bond_refined_d 0.013
r_mcbond_it 6.236
r_scbond_it 5.832
r_dihedral_angle_4_deg 18.03
r_angle_other_deg 1.25
r_gen_planes_refined 0.007
r_chiral_restr 0.095
r_mcangle_it 9.967
r_dihedral_angle_2_deg 34.193
r_mcbond_other 6.236
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

Software
Software Name Purpose
REFMAC refinement version: 5.8.0033
PDB_EXTRACT data extraction version: 3.11
ADSC data collection version: Quantum
XDS data reduction
XDS data scaling
MOLREP phasing