X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 2M Sodium Malonate, pH=7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.58 α = 90
b = 120.58 β = 90
c = 170.76 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2007-01-25
Diffraction Radiation
Monochromator Protocol
KOHZU: Double Crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2

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
1.3 50 99.2 -- 0.123 -- 8.9 -- 346171 2.0 2.0 14.6
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)
1.3 1.32 89.9 0.49 0.49 1.18 1.9 15484

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
-- 1.3 50.0 -- 0.0 487111 339183 10333 97.16 -- 0.177 0.177 0.19416 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 1.301 1.335 22367 700 23067 0.25 0.259 -- 89.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.757
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.03
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.08
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.005
r_sphericity_free 3.732
r_xyhbond_nbd_refined 0.131
r_rigid_bond_restr 3.061
r_dihedral_angle_3_deg 12.202
r_scbond_it 3.078
r_angle_refined_deg 1.15
r_symmetry_vdw_refined 0.164
r_dihedral_angle_1_deg 5.557
r_nbd_refined 0.197
r_scangle_it 3.342
r_sphericity_bonded 4.396
r_dihedral_angle_2_deg 36.853
r_symmetry_hbond_refined 0.149
r_chiral_restr 0.081
r_mcangle_it 1.356
r_nbtor_refined 0.296
r_mcbond_it 0.804
r_bond_refined_d 0.009
r_dihedral_angle_4_deg 17.004
r_metal_ion_refined 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6940
Nucleic Acid Atoms 0
Heterogen Atoms 77
Solvent Atoms 1113

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PDB_EXTRACT data extraction version: 3.000
BOS data collection
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing