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 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_scangle_it 4.479
r_scbond_it 3.625
r_mcangle_it 2.781
r_mcbond_it 2.296
r_nbd_refined 0.379
r_gen_planes_other 0.002
r_gen_planes_refined 0.011
r_chiral_restr 0.125
r_dihedral_angle_4_deg 15.733
r_dihedral_angle_3_deg 10.905
r_dihedral_angle_2_deg 41.361
r_dihedral_angle_1_deg 6.704
r_angle_other_deg 1.037
r_angle_refined_deg 1.961
r_bond_other_d 0.004
r_bond_refined_d 0.021
r_nbd_other 0.196
r_nbtor_refined 0.187
r_nbtor_other 0.092
r_xyhbond_nbd_refined 0.181
r_symmetry_vdw_refined 0.239
r_symmetry_vdw_other 0.366
r_symmetry_hbond_refined 0.188
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0019 refinement
MOLREP model building