X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 295.0
Details K/NA PHOSPHATE, MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.29 α = 90
b = 88.34 β = 90
c = 45.32 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 2000-11-29
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.979 SSRL BL9-1

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
1.7 32 99.7 -- 0.056 -- 3.7 -- 60060 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)
1.7 1.73 99.9 -- 0.591 1.4 3.7 2991

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 1.71 32.0 -- 0.0 -- 54406 2890 95.7 -- 0.18761 0.18671 0.20431 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 1.71 1.754 -- 186 3614 0.274 0.297 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.198
Anisotropic B[1][1] -0.74
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.61
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_other 0.411
r_nbd_other 0.21
r_nbd_refined 0.222
r_gen_planes_other 0.006
r_gen_planes_refined 0.008
r_chiral_restr 0.153
r_dihedral_angle_3_deg 17.04
r_dihedral_angle_1_deg 4.734
r_angle_other_deg 2.559
r_angle_refined_deg 1.784
r_bond_other_d 0.001
r_bond_refined_d 0.017
r_xyhbond_nbd_refined 0.169
r_xyhbond_nbd_other 0.036
r_symmetry_vdw_refined 0.155
r_symmetry_vdw_other 0.179
r_symmetry_hbond_refined 0.229
r_symmetry_hbond_other 0.19
r_mcbond_it 1.088
r_mcangle_it 1.989
r_scbond_it 3.054
r_scangle_it 5.076
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3112
Nucleic Acid Atoms 0
Heterogen Atoms 72
Solvent Atoms 343

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.0 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection