X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 298.0
Details NaCl, NaAcetate, PEG400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.58 α = 90
b = 66.57 β = 109.56
c = 96.92 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SBC-2 -- 2002-07-02
CCD SBC-2 -- 2002-02-13
Diffraction Radiation
Monochromator Protocol
Si 111 MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97921, 0.97935 APS 19-ID
SYNCHROTRON APS BEAMLINE 19-ID 0.97892 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
1.75 50 98.5 0.059 -- -- 4.0 109795 108148 0.0 -3.0 --
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)
1.75 1.81 88.0 0.36 -- 1.9 2.0 --

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 1.75 30.0 -- 0.0 -- 102713 5397 98.41 -- 0.1813 0.17934 0.21908 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 1.749 1.794 -- 350 6498 0.22 0.267 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.535
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.23
Anisotropic B[2][2] 0.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.27
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.327
r_nbtor_other 0.086
r_dihedral_angle_1_deg 6.073
r_chiral_restr 0.105
r_nbd_other 0.251
r_gen_planes_refined 0.008
r_mcangle_it 1.877
r_scbond_it 3.221
r_bond_other_d 0.002
r_gen_planes_other 0.003
r_mcbond_it 1.056
r_xyhbond_nbd_refined 0.174
r_symmetry_hbond_refined 0.144
r_symmetry_vdw_other 0.296
r_angle_other_deg 0.884
r_angle_refined_deg 1.662
r_nbd_refined 0.233
r_symmetry_vdw_refined 0.242
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8363
Nucleic Acid Atoms 0
Heterogen Atoms 9
Solvent Atoms 1149

Software

Software
Software Name Purpose
REFMAC refinement version: 5.1.24
d*TREK data reduction
HKL-2000 data reduction
SCALEPACK data scaling
SOLVE phasing
ARP/wARP model building