X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.2
Temperature 295.0
Details 2 M ammonium sulfate, 100 mM phosphate-citrate, and 10 mM DTT , pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.79 α = 90
b = 127.59 β = 90
c = 65.97 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-2 -- 2003-08-09
Diffraction Radiation
Monochromator Protocol
Si 111 MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9793, 0.9794, 1.008, 0.9537 APS 19-ID

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
2.5 30 99.9 0.058 -- -- 14.2 13819 13802 -- -3.0 53.1
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)
2.5 2.61 100.0 0.203 -- 13.7 -- 1697

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 2.5 30.0 -- 0.0 -- 13046 687 99.77 0.197 0.197 0.195 0.227 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 2.5 2.634 -- 106 1870 0.203 0.304 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.66
Anisotropic B[1][1] 1.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.74
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.88
r_nbd_refined 0.235
r_scangle_it 10.784
r_bond_refined_d 0.012
r_mcangle_it 5.67
r_chiral_restr 0.125
r_dihedral_angle_1_deg 0.349
r_xyhbond_nbd_refined 0.125
r_scbond_it 7.746
r_symmetry_hbond_refined 0.468
r_gen_planes_refined 0.001
r_symmetry_vdw_refined 0.251
r_mcbond_it 3.285
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2105
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 48

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing version: 2.02
RESOLVE phasing version: 2.02
REFMAC refinement version: 5.1.19