X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.2
Details CRYSTALS OF PEL10ACM WERE GROWN BY VAPOUR-PHASEDIFFUSION 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. THESE CONDITIONS FOR THE NATIVE P21 CRYSTALS WERE MODIFIED BY ADDING 25MM CACL2, WHICH RESULTED IN CRYSTALS BELONGING TO SPACE GROUP P21212

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.26 α = 90
b = 55.14 β = 90
c = 47.57 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 -- 2001-03-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX9.6 -- SRS PX9.6

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
1.5 50 99.1 0.062 -- -- 4.2 -- 45240 -- -- --
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)
1.5 1.53 98.6 0.311 -- 4.5 4.1 --

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 1.5 53.45 -- -- -- 42920 2286 99.2 -- 0.131 0.129 0.157 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 1.5 1.54 -- 150 3116 0.136 0.202 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 9.54
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.21
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.727
r_scbond_it 1.796
r_mcangle_it 1.208
r_mcbond_it 0.72
r_nbd_refined 0.221
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_chiral_restr 0.074
r_dihedral_angle_4_deg 11.792
r_dihedral_angle_3_deg 13.67
r_dihedral_angle_2_deg 35.491
r_dihedral_angle_1_deg 5.414
r_angle_other_deg 1.926
r_angle_refined_deg 1.226
r_bond_other_d 0.003
r_bond_refined_d 0.01
r_nbd_other 0.278
r_nbtor_other 0.149
r_xyhbond_nbd_refined 0.158
r_symmetry_vdw_refined 0.447
r_symmetry_vdw_other 0.24
r_symmetry_hbond_refined 0.252
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2527
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 422

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