X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 299.0
Details Ammonium Sulfate, NaCl, Tris, Glycerol, L-serine, pH 8.0, vapor diffusion, hanging drop, temperature 299K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.19 α = 90
b = 110.19 β = 90
c = 63.33 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 MARMOSAIC 225 mm CCD -- 2010-10-28
Diffraction Radiation
Monochromator Protocol
Si(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM14 0.9537 ESRF BM14

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
1.59 30 -- 0.078 -- -- 6.67 38526 38478 -- -- 27.91

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 1.59 27.55 -- 0.0 -- 38478 1910 99.84 -- 0.1618 0.1606 0.1826 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 1.59 1.631 -- 119 2659 0.301 0.324 -- 98.16
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.9204
Anisotropic B[1][1] -16.27
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -16.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 32.55
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 1.451
r_scangle_it 2.189
r_dihedral_angle_4_deg 14.75
r_dihedral_angle_3_deg 14.233
r_dihedral_angle_2_deg 31.115
r_mcbond_it 0.447
r_dihedral_angle_1_deg 5.891
r_gen_planes_refined 0.005
r_bond_refined_d 0.008
r_angle_refined_deg 1.135
r_chiral_restr 0.075
r_mcangle_it 0.856
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2119
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 106

Software

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