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 = 135.39 α = 90
b = 135.39 β = 90
c = 58.01 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
1.85 50 97.2 0.057 -- -- 6.9 -- 26504 -- -- --
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)
1.85 1.92 91.0 0.511 -- -- 6.4 2432

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 1.85 41.23 -- 0.0 -- 26282 1314 96.48 -- 0.2027 0.2007 0.2412 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 1.85 1.898 -- 87 1884 0.418 0.402 -- 99.6
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.7274
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.03
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.016
r_mcbond_it 0.856
r_gen_planes_refined 0.008
r_dihedral_angle_3_deg 14.385
r_mcangle_it 1.539
r_angle_refined_deg 1.528
r_chiral_restr 0.115
r_dihedral_angle_2_deg 35.689
r_dihedral_angle_1_deg 5.875
r_dihedral_angle_4_deg 20.148
r_scangle_it 4.382
r_scbond_it 2.627
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1761
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 130

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