X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 293.0
Details 0.1 M sodium phosphate, pH 5.5, 10% w/v PEG6000, cryoprotectant: mother liquor + 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80.91 α = 90
b = 80.91 β = 90
c = 33.24 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- --
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LNLS BEAMLINE D03B-MX1 -- LNLS D03B-MX1

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
2.3 40.46 99.8 -- 0.093 -- 3.0 3608 3608 -- -- --
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)
2.3 2.42 100.0 0.17 0.17 4.4 3.0 530

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 2.3 40.45 -- 0.0 -- 3606 330 99.78 -- 0.2086 0.2007 0.2875 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 2.3 2.36 -- 19 257 0.18 0.248 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.1289
Anisotropic B[1][1] 0.07
Anisotropic B[1][2] 0.04
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.11
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.006
r_dihedral_angle_1_deg 9.017
r_dihedral_angle_2_deg 37.796
r_chiral_restr 0.105
r_angle_refined_deg 1.655
r_dihedral_angle_3_deg 18.288
r_bond_refined_d 0.014
r_dihedral_angle_4_deg 18.08
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 808
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 98

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.3.20
PHASER phasing version: 2.1.4
REFMAC refinement version: 5.6.0117
PDB_EXTRACT data extraction version: 3.11
Marresearch data collection