X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.1
Details PROTEIN AT 45 MG/ML IN 10MM SODIUM PHOSPHATE WITH 0.25M SODIUM L-TARTRATE (PH=7.1) AND 10% (V/V) GLYCEROL; CRYSTALS GROWN AT 22C

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.88 α = 90
b = 57.88 β = 90
c = 149.95 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC TOROIDAL FOCUSING MIRROR 2007-08-22
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
0.94 20 99.0 0.04 -- -- 6.1 -- 163884 -- 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)
0.94 0.96 100.0 0.59 -- 3.1 6.7 --

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 0.94 20.0 -- -- -- 155413 8230 98.9 -- 0.125 0.124 0.134 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 0.94 0.96 -- 627 11400 0.183 0.21 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.59
Anisotropic B[1][1] 0.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.34
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 3.067
r_scbond_it 2.343
r_mcangle_it 2.007
r_mcbond_it 1.384
r_nbd_refined 0.28
r_gen_planes_refined 0.009
r_chiral_restr 0.098
r_dihedral_angle_4_deg 11.785
r_dihedral_angle_3_deg 10.564
r_dihedral_angle_2_deg 35.739
r_dihedral_angle_1_deg 6.665
r_angle_refined_deg 1.552
r_bond_refined_d 0.01
r_nbtor_refined 0.313
r_xyhbond_nbd_refined 0.122
r_symmetry_vdw_refined 0.227
r_symmetry_hbond_refined 0.122
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1545
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 414

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