X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.2
Details CRYSTALS OF PEL10ACM WERE GROWN BY VAPOUR-PHASE DIFFUSION USING THE HANGING-DROP METHOD WITH SCREENING AS DESCRIBED BY BRZOZOWSKI & WALTON (2001 [[BRZOZOWSKI, A.M. & WALTON, J.(2001). J. APPL. CRYST. 34, 97-101.]] ). THE PROTEIN CONCENTRATION WAS 30 MG ML-1 IN NA MES BUFFER PH 5.2 CONTAINING KSCN AT A CONCENTRATION OF 200 MM. THE PRECIPITANT WAS 20%(W/V) MONOMETHYL POLYETHYLENEGLYCOL 2000. 25MM CACL2 AND 20MM TRIGALACTURONIC ACID WERE ALSO ADDED.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.43 α = 90
b = 54.92 β = 90
c = 47.19 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
CCD ADSC -- 2001-02-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 -- ESRF ID29

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
2.05 50 79.2 0.073 -- -- 3.5 -- 14154 -- -- --
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)
2.05 2.12 29.3 0.32 -- 2.1 1.6 --

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
OTHER 2.05 52.7 -- -- -- 13414 705 79.2 -- 0.176 0.173 0.228 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 2.05 2.1 -- 11 339 0.163 0.302 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.88
Anisotropic B[1][1] -0.13
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.11
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.99
r_scbond_it 1.882
r_mcangle_it 1.076
r_mcbond_it 0.586
r_nbd_refined 0.209
r_gen_planes_refined 0.005
r_chiral_restr 0.09
r_dihedral_angle_4_deg 20.694
r_dihedral_angle_3_deg 15.148
r_dihedral_angle_2_deg 35.377
r_dihedral_angle_1_deg 5.248
r_angle_refined_deg 1.316
r_bond_refined_d 0.012
r_xyhbond_nbd_refined 0.155
r_metal_ion_refined 0.171
r_symmetry_vdw_refined 0.269
r_symmetry_hbond_refined 0.264
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2504
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 171

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
REFMAC 5.1.08 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.1.08 refinement