X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 298.0
Details (NH3)4SO4, MES, LiCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.6 α = 90
b = 108.6 β = 90
c = 201.03 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirros 2004-04-11
CCD ADSC QUANTUM 315 -- 2004-06-09
Diffraction Radiation
Monochromator Protocol
Si(111) MAD
Veri-max SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54 -- --
SYNCHROTRON NSLS BEAMLINE X29A 1.0772, 1.0723, 1.0540 NSLS X29A

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 99 99.4 0.062 -- -- -- -- 20508 -- -- --
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 2.38 94.7 0.352 -- -- -- 1924

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
MAD 2.3 30.0 -- 0.0 -- 19447 1050 99.65 -- 0.21411 0.21089 0.27466 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 -- 84 1344 0.241 0.354 -- 95.84
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.19
Anisotropic B[1][1] -1.66
Anisotropic B[1][2] -0.83
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.66
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.48
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 1.211
r_scangle_it 3.041
r_dihedral_angle_2_deg 36.496
r_chiral_restr 0.091
r_dihedral_angle_4_deg 16.2
r_bond_refined_d 0.013
r_dihedral_angle_1_deg 6.846
r_angle_refined_deg 1.398
r_scbond_it 1.883
r_gen_planes_refined 0.005
r_dihedral_angle_3_deg 16.201
r_mcbond_it 0.639
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3163
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 204

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing version: 2.03
RESOLVE phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.006
ADSC data collection version: Quantum