X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 298.0
Details 2.3 M Ammoniumsulfate, 0.1M Citric acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 73.89 α = 90
b = 73.89 β = 90
c = 183.35 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 MIRROR 2006-04-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.980 ESRF ID23-1

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
1.6 68 99.8 -- 0.061 -- 3.8 -- 67896 -- -- --
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)
1.6 1.69 100.0 -- 0.407 2.8 -- --

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 1.6 57.54 0.0 0.0 -- 64263 3451 99.73 -- 0.18416 0.18235 0.21852 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 1.6 1.642 -- 256 4687 0.245 0.342 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.752
Anisotropic B[1][1] 0.38
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.38
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.77
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 4.251
r_sphericity_free 4.331
r_rigid_bond_restr 2.481
r_scangle_it 3.752
r_scbond_it 2.956
r_mcangle_it 1.75
r_mcbond_it 1.203
r_nbd_refined 0.195
r_gen_planes_refined 0.005
r_chiral_restr 0.09
r_dihedral_angle_4_deg 16.707
r_dihedral_angle_3_deg 13.139
r_dihedral_angle_2_deg 31.638
r_dihedral_angle_1_deg 5.639
r_angle_refined_deg 1.229
r_bond_refined_d 0.011
r_nbtor_refined 0.3
r_xyhbond_nbd_refined 0.125
r_symmetry_vdw_refined 0.213
r_symmetry_hbond_refined 0.124
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.37
Luzzati Sigma A (Observed) 0.35
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.39
Luzzati Sigma A (R-Free Set) 0.32
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2764
Nucleic Acid Atoms 0
Heterogen Atoms 37
Solvent Atoms 487

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.3.0008 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.3.0008 refinement