X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 293.0
Details 20mM MgCl2, 14% PEG3000, 80mM sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 153.26 α = 90
b = 153.26 β = 90
c = 160.17 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2005-11-12
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X26C 1.1 NSLS X26C

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
3.3 50 99.9 0.138 -- -- 7.8 33350 33350 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)
3.3 3.42 100.0 0.548 -- -- 7.9 3332

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 3.3 10.0 -- 0.0 33350 31873 1580 100.0 0.207 0.21 0.205 0.258 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 3.3 3.376 2153 105 2048 0.264 0.324 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 71.961
Anisotropic B[1][1] 1.97
Anisotropic B[1][2] 0.98
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.97
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.95
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 4.078
r_gen_planes_other 0.001
r_bond_other_d 0.003
r_xyhbond_nbd_other 0.069
r_scbond_it 1.255
r_nbtor_refined 0.182
r_symmetry_hbond_refined 0.149
r_angle_other_deg 0.796
r_angle_refined_deg 1.37
r_symmetry_vdw_other 0.189
r_dihedral_angle_3_deg 16.42
r_mcangle_it 2.626
r_nbd_other 0.18
r_nbtor_other 0.085
r_dihedral_angle_2_deg 34.248
r_mcbond_other 0.229
r_gen_planes_refined 0.003
r_scangle_it 2.174
r_dihedral_angle_4_deg 14.052
r_symmetry_vdw_refined 0.11
r_nbd_refined 0.209
r_mcbond_it 1.613
r_xyhbond_nbd_refined 0.147
r_chiral_restr 0.082
r_bond_refined_d 0.019
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8803
Nucleic Acid Atoms 343
Heterogen Atoms 32
Solvent Atoms 0

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
REFMAC refinement
PDB_EXTRACT data extraction version: 1.701
HKL-2000 data reduction
AMoRE phasing