X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.2
Temperature 293.0
Details 0.8M phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.1 α = 90
b = 106.61 β = 101.92
c = 47.54 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2008-02-08
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 1.0723 ESRF ID23-1

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
1.2 50 99.3 0.081 -- -- 5.0 -- 135290 -- -- --
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)
1.2 1.24 98.4 0.375 -- 3.5 5.0 13388

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 1.5 19.2 -- -- -- 66447 3441 99.78 -- 0.14537 0.14379 0.17646 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 1.5 1.539 -- 254 4853 0.142 0.178 -- 99.49
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 10.463
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.221
r_symmetry_hbond_refined 0.193
r_mcbond_it 1.65
r_dihedral_angle_3_deg 13.176
r_dihedral_angle_4_deg 15.538
r_chiral_restr 0.079
r_bond_refined_d 0.011
r_dihedral_angle_1_deg 3.882
r_dihedral_angle_2_deg 40.183
r_nbtor_refined 0.315
r_scangle_it 4.15
r_scbond_it 2.721
r_xyhbond_nbd_refined 0.189
r_symmetry_vdw_refined 0.251
r_mcangle_it 2.429
r_angle_refined_deg 1.301
r_gen_planes_refined 0.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3891
Nucleic Acid Atoms 0
Heterogen Atoms 148
Solvent Atoms 751

Software

Software
Software Name Purpose
DNA data collection
PHASER phasing
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling