X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.15
Details 100 mM Mes-KOH (pH 6.5), 200 mM KCl, 75 mM NH4Cl, 15 mM MgCl2, and 26% (vol/vol) 2-Methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, 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
1 100
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.99 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 29.7 91.4 -- -- -- -- 234683 234683 0.0 0.0 --
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 3.2 95.1 -- 0.691 1.47 -- --

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 3.1 29.67 -- 0.0 234682 234682 11726 91.35 0.1873 0.1873 0.1852 0.2262 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 3.1 3.18 -- 869 16852 0.296 0.319 -- 95.14
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 83.2593
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] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 10.609
r_mcbond_other 6.718
r_bond_refined_d 0.01
r_bond_other_d 0.003
r_angle_refined_deg 1.751
r_angle_other_deg 1.26
r_dihedral_angle_1_deg 8.601
r_dihedral_angle_2_deg 34.871
r_dihedral_angle_3_deg 23.112
r_dihedral_angle_4_deg 20.012
r_chiral_restr 0.101
r_gen_planes_refined 0.008
r_gen_planes_other 0.001
r_mcbond_it 6.718
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19120
Nucleic Acid Atoms 32485
Heterogen Atoms 427
Solvent Atoms 0

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHENIX Structure Solution
REFMAC 5.8.0031 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.8.0031 refinement