X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 1.4M NACITRATE, 0.1M TRIS PH 8.5, 0.01M ATP, CRYO-XYLITOL, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.46 α = 90
b = 62.74 β = 99.91
c = 93.45 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2005-06-28
Diffraction Radiation
Monochromator Protocol
KOHZU DOUBLE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A .9791 NSLS X4A

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
1.9 20 98.0 0.065 -- -- 3.2 57959 57959 0.0 -3.0 --
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)
1.9 1.97 96.2 0.281 -- 2.37 2.5 5669

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 1.9 20.0 -3.0 0.0 57813 57813 2911 98.01 0.20308 0.20308 0.20111 0.23996 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 1.9 1.949 -- 195 3957 0.287 0.331 -- 96.42
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.881
Anisotropic B[1][1] -0.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.06
Anisotropic B[2][2] 1.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.11
RMS Deviations
Key Refinement Restraint Deviation
r_angle_other_deg 0.858
r_gen_planes_refined 0.003
r_gen_planes_other 0.001
r_angle_refined_deg 1.18
r_scbond_it 1.91
r_nbd_other 0.168
r_symmetry_vdw_refined 0.151
r_symmetry_vdw_other 0.205
r_bond_refined_d 0.011
r_mcbond_it 1.104
r_symmetry_hbond_refined 0.149
r_nbtor_refined 0.159
r_chiral_restr 0.067
r_dihedral_angle_2_deg 38.176
r_nbd_refined 0.193
r_mcangle_it 1.168
r_bond_other_d 0.001
r_xyhbond_nbd_refined 0.177
r_nbtor_other 0.079
r_mcbond_other 0.138
r_dihedral_angle_1_deg 5.833
r_scangle_it 2.712
r_dihedral_angle_4_deg 12.511
r_dihedral_angle_3_deg 13.798
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4815
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 409

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0016
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing