X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.3
Details MICROBATCH METHOD; PROTEIN AT 40.5 MG/ML IN 10MM SODIUM PHOSPHATE WITH 250 MM SODIUM MESO-TARTRATE (PH=7.3) AND 2.5% (V/V) GLYCEROL; CRYSTALS GROWN AT 4 C.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.81 α = 90
b = 63.91 β = 90
c = 71.68 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 2008-04-24
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
1.08 20 98.1 0.06 -- -- 5.1 -- 85314 -- 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)
1.08 1.1 79.2 0.33 -- 2.0 2.0 --

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 1.08 19.9 -- -- -- 80942 4262 100.0 -- 0.129 0.128 0.143 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 1.08 1.11 -- 255 4936 0.188 0.199 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 11.49
Anisotropic B[1][1] -1.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.56
RMS Deviations
Key Refinement Restraint Deviation
r_nbd_refined 0.206
r_nbtor_refined 0.311
r_xyhbond_nbd_refined 0.187
r_mcbond_it 1.79
r_scangle_it 3.685
r_mcangle_it 2.353
r_dihedral_angle_4_deg 17.653
r_chiral_restr 0.108
r_angle_refined_deg 1.727
r_symmetry_hbond_refined 0.103
r_bond_refined_d 0.015
r_gen_planes_refined 0.011
r_dihedral_angle_3_deg 10.928
r_dihedral_angle_2_deg 38.066
r_dihedral_angle_1_deg 7.203
r_symmetry_vdw_refined 0.206
r_scbond_it 2.946
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1551
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 355

Software

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