X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.7
Temperature 298.0
Details 1.6 M Sodium citrate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.67 α = 90
b = 83.67 β = 90
c = 35.88 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 crystal 2005-03-07
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X29A 0.9793 NSLS X29A

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
1.45 50 98.7 0.07 0.07 -- 10.9 25306 24796 0.0 0.0 23.3
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)
1.45 1.5 96.3 0.441 0.441 4.5 9.7 2416

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
SAD 1.45 50.0 0.0 0.0 25306 24796 1252 98.74 0.17 0.17 0.169 0.189 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 1.45 1.488 1798 91 1707 0.205 0.27 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.648
Anisotropic B[1][1] -0.2
Anisotropic B[1][2] -0.1
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.3
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.671
r_scbond_it 1.791
r_mcangle_it 1.195
r_mcbond_it 0.716
r_symmetry_hbond_refined 0.151
r_bond_refined_d 0.008
r_angle_refined_deg 1.141
r_dihedral_angle_1_deg 6.0
r_dihedral_angle_2_deg 29.999
r_dihedral_angle_3_deg 12.112
r_dihedral_angle_4_deg 7.742
r_chiral_restr 0.082
r_gen_planes_refined 0.005
r_nbd_refined 0.199
r_nbtor_refined 0.307
r_xyhbond_nbd_refined 0.096
r_symmetry_vdw_refined 0.212
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1029
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 170

Software

Computing
Computing Package Purpose
HKL Data Reduction (data scaling)
SOLVE, PHASER Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 1.701 data extraction
REFMAC5 refinement
RESOLVE version: 2.08 density modification
SOLVE version: 2.08 phasing
Phaser molecular replacement
HKL data processing