3VI6

Crystal Structure of human ribosomal protein L30e


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 293.0
Details 0.3M potassium chrolide, 1mM EDTA, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.28 α = 90
b = 56.28 β = 90
c = 203.63 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 crystals 2010-01-21
Diffraction Radiation
Monochromator Protocol
silicon SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A

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
1.59 50 99.6 0.052 -- -- 10.7 -- 16978 0.0 0.0 17.9
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)
1.59 1.62 98.3 0.31 -- 8.2 10.1 814

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 1.59 50.0 -- -- -- 16106 864 99.48 -- 0.19114 0.18985 0.21625 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 1.595 1.636 -- 57 1172 0.217 0.257 -- 98.4
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.046
Anisotropic B[1][1] 0.79
Anisotropic B[1][2] 0.39
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.79
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.18
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.157
r_dihedral_angle_3_deg 13.146
r_rigid_bond_restr 1.25
r_dihedral_angle_4_deg 31.54
r_scbond_it 2.909
r_chiral_restr 0.079
r_dihedral_angle_2_deg 26.477
r_mcbond_it 0.852
r_scangle_it 4.484
r_dihedral_angle_1_deg 4.774
r_mcangle_it 1.632
r_bond_refined_d 0.008
r_gen_planes_refined 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 753
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 83

Software

Software
Software Name Purpose
SERGUI data collection
REFMAC refinement version: 5.5.0102
HKL-2000 data reduction
SCALEPACK data scaling