X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details Na Acetate, Imidazole, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.59 α = 90
b = 96.59 β = 90
c = 80.56 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-02-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 -- ALS 8.3.1

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
2 84.57 99.7 0.065 0.065 -- 4.0 29618 29538 1.5 1.5 --
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)
2.0 2.05 99.2 0.758 0.758 0.8 3.5 --

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 2.0 84.51 -- 1.5 29618 27964 1495 99.47 0.189 0.188 0.188 0.211 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 2.0 2.052 -- 111 2025 0.289 0.308 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.693
Anisotropic B[1][1] 0.95
Anisotropic B[1][2] 0.48
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.95
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.43
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.467
r_scbond_it 1.45
r_mcangle_it 1.103
r_mcbond_it 0.583
r_symmetry_hbond_refined 0.115
r_symmetry_vdw_other 0.267
r_symmetry_vdw_refined 0.135
r_bond_refined_d 0.009
r_bond_other_d 0.002
r_angle_refined_deg 1.255
r_angle_other_deg 0.8
r_dihedral_angle_1_deg 2.915
r_chiral_restr 0.084
r_gen_planes_refined 0.005
r_gen_planes_other 0.004
r_nbd_refined 0.198
r_nbd_other 0.232
r_nbtor_other 0.079
r_xyhbond_nbd_refined 0.156
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2230
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 170

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.1.25 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 1.600 data extraction
REFMAC5 version: 5.1.25 refinement
SCALA data processing