X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.3
Details MICROBATCH METHOD; PROTEIN AT 26 MG/ML IN 10MM SODIUM PHOSPHATE WITH 62.5 MM SODIUM MESO-TARTRATE (PH=7.3) AND 2.5% (V/V) GLYCEROL; CRYSTALS GROWN AT 19 C.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.89 α = 90
b = 54.52 β = 90
c = 70.87 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD TOROIDAL FOCUSING MIRROR 2008-04-22
Diffraction Radiation
Monochromator Protocol
SI(111) CHANNEL CUT SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X6A -- NSLS X6A

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
0.95 12 99.5 0.06 -- -- 5.9 -- 123941 -- 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)
0.95 0.97 100.0 -- -- -- 5.6 --

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 0.95 11.85 -- -- -- 117584 6208 100.0 -- 0.118 0.117 0.136 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 0.95 0.97 -- 461 8576 0.244 0.249 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 8.39
Anisotropic B[1][1] 0.31
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.42
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 2.296
r_symmetry_vdw_other 0.366
r_gen_planes_refined 0.011
r_gen_planes_other 0.002
r_nbd_refined 0.379
r_bond_refined_d 0.021
r_nbd_other 0.196
r_symmetry_hbond_refined 0.188
r_scangle_it 4.479
r_dihedral_angle_3_deg 10.905
r_symmetry_vdw_refined 0.239
r_dihedral_angle_4_deg 15.733
r_chiral_restr 0.125
r_angle_refined_deg 1.961
r_angle_other_deg 1.037
r_mcangle_it 2.781
r_nbtor_refined 0.187
r_scbond_it 3.625
r_xyhbond_nbd_refined 0.181
r_dihedral_angle_2_deg 41.361
r_bond_other_d 0.004
r_nbtor_other 0.092
r_dihedral_angle_1_deg 6.704
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1551
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 341

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing