X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.3
Temperature 277.0
Details 0.1M sodium citric, 0.2M sodium potassium tartrate, 1.6M ammonium sulfate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 64.72 α = 90
b = 81.7 β = 90
c = 281.88 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 QUANTUM 210 mirrors 2008-05-24
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A

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
2.8 50 98.1 0.118 0.118 -- 12.5 37885 37165 1.0 1.0 --
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)
2.8 2.9 84.7 0.343 0.343 2.7 4.8 3139

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 2.8 50.0 1.0 1.0 36009 35307 1850 98.05 -- 0.22672 0.22475 0.26438 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 2.8 2.873 -- 113 2149 0.319 0.352 -- 83.38
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.434
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.61
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.63
RMS Deviations
Key Refinement Restraint Deviation
r_symmetry_hbond_refined 0.153
r_gen_planes_refined 0.003
r_rigid_bond_restr 1.275
r_scbond_it 1.302
r_dihedral_angle_4_deg 14.871
r_chiral_restr 0.085
r_nbd_refined 0.196
r_mcbond_it 0.855
r_sphericity_free 0.78
r_xyhbond_nbd_refined 0.125
r_dihedral_angle_3_deg 19.127
r_symmetry_vdw_refined 0.231
r_sphericity_bonded 0.406
r_angle_refined_deg 1.087
r_scangle_it 2.016
r_bond_refined_d 0.008
r_dihedral_angle_1_deg 5.463
r_nbtor_refined 0.305
r_mcangle_it 1.539
r_dihedral_angle_2_deg 35.057
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9448
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 356

Software

Software
Software Name Purpose
HKL-2000 data collection
CNS refinement
REFMAC refinement version: 5.2.0019
HKL-2000 data reduction
HKL-2000 data scaling
CNS phasing