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 -- --
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 NSLS BEAMLINE X6A -- NSLS X6A
SYNCHROTRON ESRF BEAMLINE ID15B -- ESRF ID15B

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_scangle_it 3.548
r_scbond_it 2.711
r_mcangle_it 2.15
r_mcbond_it 1.482
r_nbd_refined 0.216
r_gen_planes_refined 0.009
r_chiral_restr 0.096
r_dihedral_angle_4_deg 14.158
r_dihedral_angle_3_deg 11.284
r_dihedral_angle_2_deg 36.254
r_dihedral_angle_1_deg 6.976
r_angle_refined_deg 1.569
r_bond_refined_d 0.011
r_nbtor_refined 0.315
r_xyhbond_nbd_refined 0.14
r_symmetry_vdw_refined 0.207
r_symmetry_hbond_refined 0.14
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

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