X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 4.6
Temperature 291.0
Details 0.1 M sodium acetate, 3.2 M sodium chloride, 5%(v/v) glycerol, pH 4.6, vapor diffusion, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 135.55 α = 90
b = 135.55 β = 90
c = 57.77 γ = 120
Symmetry
Space Group P 63 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LNLS BEAMLINE W01B-MX2 -- LNLS W01B-MX2

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
1.7 50 98.4 0.066 -- -- 8.8 -- 34286 -- -- --
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)
1.7 1.76 98.3 0.455 -- -- 4.8 3352

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 1.7 41.17 -- 0.0 -- 34157 1717 98.05 -- 0.1788 0.1776 0.2039 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 1.7 1.744 -- 113 2334 0.359 0.425 -- 97.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.781
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_angle_refined_deg 1.473
r_bond_refined_d 0.014
r_mcangle_it 1.513
r_chiral_restr 0.109
r_gen_planes_refined 0.009
r_mcbond_it 0.837
r_dihedral_angle_4_deg 8.438
r_dihedral_angle_1_deg 5.963
r_scangle_it 4.048
r_dihedral_angle_2_deg 34.741
r_scbond_it 2.413
r_dihedral_angle_3_deg 13.356
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1761
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 154

Software

Software
Software Name Purpose
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data reduction
HKL-2000 data scaling