X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.1
Details MICROBATCH METHOD; PROTEIN AT 45 MG/ML IN 10MM SODIUM PHOSPHATE WITH 0.25M SODIUM DL-TARTRATE (PH=7.1) AND 10% (V/V) GLYCEROL; CRYSTALS GROWN AT 6 C

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.92 α = 90
b = 57.92 β = 90
c = 149.95 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC CCD -- --
IMAGE PLATE MARRESEARCH -- 2007-09-20
Diffraction Radiation
Monochromator Protocol
-- --
BRAGG-MONO SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID15B -- ESRF ID15B
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
1.1 20 99.7 0.06 -- -- 8.2 -- 104165 -- 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)
1.1 1.12 100.0 0.63 -- 2.1 8.5 --

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 1.1 19.75 -- -- -- 98770 5196 100.0 -- 0.126 0.125 0.14 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 1.1 1.13 -- 367 7206 0.162 0.173 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.08
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_mcbond_it 1.482
r_bond_refined_d 0.011
r_scbond_it 2.711
r_dihedral_angle_4_deg 14.158
r_symmetry_hbond_refined 0.14
r_chiral_restr 0.096
r_gen_planes_refined 0.009
r_nbtor_refined 0.315
r_nbd_refined 0.216
r_mcangle_it 2.15
r_xyhbond_nbd_refined 0.14
r_scangle_it 3.548
r_symmetry_vdw_refined 0.207
r_angle_refined_deg 1.569
r_dihedral_angle_3_deg 11.284
r_dihedral_angle_2_deg 36.254
r_dihedral_angle_1_deg 6.976
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1545
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 418

Software

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