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_chiral_restr 0.105
r_dihedral_angle_4_deg 18.08
r_dihedral_angle_3_deg 18.288
r_dihedral_angle_2_deg 37.796
r_dihedral_angle_1_deg 9.017
r_angle_refined_deg 1.655
r_bond_refined_d 0.014
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

Computing
Computing Package Purpose
Marresearch Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.6.0117 refinement
Phaser version: 2.1.4 molecular replacement
SCALA version: 3.3.20 data reduction
Mosflm data collection