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 D-TARTRATE (PH=7.1) AND 10% (V/V) GLYCEROL; CRYSTALS GROWN AT 22 C

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.94 α = 90
b = 54.3 β = 90
c = 70.81 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 2007-08-23
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
1.04 20 99.0 0.05 -- -- 7.2 -- 93952 -- 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)
1.04 1.06 97.7 0.7 -- 2.2 6.0 --

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 1.04 16.72 -- -- -- 89156 4704 100.0 -- 0.129 0.128 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 1.04 1.07 -- 352 6391 0.184 0.209 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 13.11
Anisotropic B[1][1] 0.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.14
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 18.23
r_mcbond_it 1.665
r_scangle_it 3.899
r_dihedral_angle_3_deg 10.963
r_chiral_restr 0.101
r_xyhbond_nbd_refined 0.12
r_dihedral_angle_2_deg 40.544
r_scbond_it 2.926
r_angle_refined_deg 1.56
r_nbtor_refined 0.312
r_bond_refined_d 0.012
r_gen_planes_refined 0.009
r_mcangle_it 2.382
r_symmetry_vdw_refined 0.208
r_dihedral_angle_1_deg 6.409
r_nbd_refined 0.249
r_symmetry_hbond_refined 0.103
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1551
Nucleic Acid Atoms 0
Heterogen Atoms 18
Solvent Atoms 308

Software

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