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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
1O4U
Crystal structure of a nicotinate nucleotide pyrophosphorylase (tm1645) from thermotoga maritima at 2.50 A resolution
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
Download Files
FASTA Sequence
PDB File (Text)
PDB File (gz)
PDBx/mmCIF File
PDBx/mmCIF File (gz)
PDBML/XML File
PDBML/XML File (gz)
Structure Factor (Text)
Structure Factor (gz)
Biological Assembly (gz) (A+S)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Sitting Drop Nanodrop
pH
6
Temperature
293.0
Details
10% PEG-6000, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 96.37
α = 90
b = 126.12
β = 90
c = 138.37
γ = 90
Symmetry
Space Group
I 2 2 2
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
ADSC QUANTUM 315
flat mirror
2002-06-12
Diffraction Radiation
Monochromator
Protocol
single crystal Si(111) bent monochromator
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
SSRL BEAMLINE BL11-1
--
SSRL
BL11-1
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
2.5
38.29
99.2
--
0.081
--
4.3
29194
29194
--
--
63.66
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)
2.5
2.57
93.2
--
0.546
2.0
3.9
2002
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
2.5
38.29
--
0.0
--
27683
1510
98.96
--
0.216
0.21295
0.27225
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
2.501
2.566
--
114
1886
0.33
0.375
--
--
Temperature Factor Modeling
Temperature Factor
Value
Isotropic Thermal Model
ISOTROPIC
Mean Isotropic B
37.427
Anisotropic B[1][1]
3.48
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
0.4
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-3.88
RMS Deviations
Key
Refinement Restraint Deviation
r_angle_refined_deg
1.516
r_chiral_restr
0.084
r_symmetry_vdw_refined
0.254
r_dihedral_angle_2_deg
39.854
r_angle_other_deg
0.835
r_xyhbond_nbd_refined
0.182
r_nbd_other
0.178
r_symmetry_hbond_refined
0.188
r_gen_planes_other
0.001
r_mcbond_it
0.728
r_nbtor_other
0.089
r_bond_refined_d
0.017
r_nbd_refined
0.225
r_bond_other_d
0.001
r_dihedral_angle_3_deg
17.661
r_dihedral_angle_4_deg
19.228
r_scbond_it
2.092
r_symmetry_vdw_other
0.296
r_dihedral_angle_1_deg
6.607
r_gen_planes_refined
0.005
r_mcangle_it
1.388
r_scangle_it
3.795
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
4074
Nucleic Acid Atoms
0
Heterogen Atoms
0
Solvent Atoms
113
Software
Software
Software Name
Purpose
MOSFLM
data reduction
SCALA
data scaling version: 4.2)
MOLREP
phasing
REFMAC
refinement
CCP4
data scaling version: (SCALA)