X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 295.0
Details Sa MtgA E100Q at 10 mg/ml was mixed with 1mM Moenomycin and 1mM MnCl2 and incubated on ice for ~3 hours. Precipitated material was removed by centrifugation at 16,000xg for 5 minutes. The Mmoenomycin complex was crystallized by hanging drop vapor diffusion, mixing the protein 1:1 with a reservoir solution containing 0.1M Na Acetate pH 4.6, 0.2M NaCl, 30% MPD at 22oC. Hexagonal plate crystals formed in 1 week., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 114.42 α = 90
b = 114.42 β = 90
c = 128.84 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944 Rigaku Varimax HF optics 2007-09-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E DW 1.54 -- --

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
2.1 23.12 99.9 -- 0.173 -- 3.9 -- 45531 2.0 2.0 --
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)
2.1 2.2 100.0 -- 0.381 3.2 3.8 4606

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 2.1 23.12 2.0 2.0 45531 18121 963 99.69 -- 0.19183 0.18917 0.24379 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 2.1 2.155 -- 75 1321 0.219 0.282 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.033
Anisotropic B[1][1] -2.03
Anisotropic B[1][2] -1.02
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.05
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 3.675
r_dihedral_angle_3_deg 14.695
r_angle_refined_deg 1.8
r_dihedral_angle_4_deg 21.85
r_scbond_it 5.623
r_gen_planes_refined 0.008
r_mcbond_it 2.401
r_scangle_it 7.279
r_bond_refined_d 0.019
r_chiral_restr 0.169
r_dihedral_angle_1_deg 5.865
r_dihedral_angle_2_deg 37.965
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1708
Nucleic Acid Atoms 0
Heterogen Atoms 105
Solvent Atoms 124

Software

Software
Software Name Purpose
CrystalClear data collection
AMoRE phasing
REFMAC refinement version: 5.4.0069
HKL-2000 data reduction
HKL-2000 data scaling