X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 295.0
Details 100 mM Na HEPES, 100 mM sodium chloride, 30%(v/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.31 α = 90
b = 85.31 β = 90
c = 113.97 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE -- 2001-04-24
Diffraction Radiation
Monochromator Protocol
DOUBLE CRYSTAL MONOCHROMATOR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25

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
2.5 50 92.5 0.052 -- -- 8.1 8304 8304 -- -3.0 61.3
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)
2.5 2.6 61.0 0.169 -- 2.6 -- 526

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 2.5 74.54 0.0 0.0 7722 7722 455 91.38 -- 0.25505 0.25308 0.28756 RANDOM, 5.5%
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 2.5 2.59 522 29 464 0.297 0.338 -- 61.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC, WITH TLS
Mean Isotropic B 31.215
Anisotropic B[1][1] -0.93
Anisotropic B[1][2] -0.47
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.4
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_refined 0.158
r_chiral_restr 0.094
r_bond_refined_d 0.018
r_scbond_it 3.427
r_dihedral_angle_1_deg 4.662
r_nbd_refined 0.24
r_gen_planes_refined 0.006
r_symmetry_hbond_refined 0.208
r_mcangle_it 3.012
r_mcbond_it 1.834
r_angle_refined_deg 1.577
r_symmetry_vdw_refined 0.244
r_scangle_it 5.178
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.432
Luzzati Resolution Cutoff (Low) 10.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 830
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 47

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
REFMAC refinement version: 5.0