X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 295.0
Details 0.8 M potassium sodium tartrate, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 146.41 α = 90
b = 146.41 β = 90
c = 125.6 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2004-10-31
CCD ADSC QUANTUM 4 -- 2004-07-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X26C 1.25360 NSLS X26C
SYNCHROTRON NSLS BEAMLINE X26C 0.9745, 0.97971 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
2.5 50 99.1 0.099 -- -- -- -- 47401 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)
2.5 2.54 85.4 0.543 -- -- -- --

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 25.0 -- 0.0 47073 44680 2393 98.65 0.232 0.232 0.229 0.276 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 2.499 2.563 -- 153 2903 0.408 0.452 -- 88.48
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 57.033
Anisotropic B[1][1] -0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_vdw_refined 0.221
r_angle_refined_deg 1.592
r_mcangle_it 0.93
r_bond_refined_d 0.015
r_dihedral_angle_4_deg 16.579
r_dihedral_angle_2_deg 37.302
r_symmetry_hbond_refined 0.26
r_chiral_restr 0.108
r_gen_planes_refined 0.007
r_dihedral_angle_3_deg 20.43
r_xyhbond_nbd_refined 0.148
r_nbd_refined 0.225
r_nbtor_refined 0.302
r_scbond_it 1.401
r_scangle_it 2.206
r_dihedral_angle_1_deg 8.959
r_mcbond_it 0.541
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6693
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 150

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing version: 2.03
RESOLVE phasing version: 2.03
REFMAC refinement
PDB_EXTRACT data extraction version: 1.700
HKL-2000 data reduction