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 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_scangle_it 3.685
r_scbond_it 2.946
r_mcangle_it 2.353
r_mcbond_it 1.79
r_nbd_refined 0.206
r_gen_planes_refined 0.011
r_chiral_restr 0.108
r_dihedral_angle_4_deg 17.653
r_dihedral_angle_3_deg 10.928
r_dihedral_angle_2_deg 38.066
r_dihedral_angle_1_deg 7.203
r_angle_refined_deg 1.727
r_bond_refined_d 0.015
r_nbtor_refined 0.311
r_xyhbond_nbd_refined 0.187
r_symmetry_vdw_refined 0.206
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 28
Solvent Atoms 355

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