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139717
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
3D View
Annotations
Sequence
Sequence Similarity
Structure Similarity
Experiment
1N4G
Structure of CYP121, a Mycobacterial P450, in Complex with Iodopyrazole
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)
X-RAY DIFFRACTION Experimental Data & Validation
X-ray Experimental Help
Crystallization
Crystalization Experiments
Method
Vapor Diffusion Hanging Drop
pH
6.3
Temperature
277.0
Details
ammonium sulphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Data
Unit Cell
Length (Å)
Angle (°)
a = 78.72
α = 90
b = 78.72
β = 90
c = 268.24
γ = 120
Symmetry
Space Group
P 65 2 2
Diffraction
Diffraction Experiment
ID #
Data Collection Temperature
1
100
Diffraction Detector
Detector
Diffraction Type
Details
Collection Date
CCD
MARRESEARCH
--
2002-06-15
Diffraction Radiation
Monochromator
Protocol
diamond
SINGLE WAVELENGTH
Diffraction Detector Source
Source
Type
Wavelength List
Synchrotron Site
Beamline
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X11
0.9
EMBL/DESY, Hamburg
X11
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
1.8
20
95.2
0.072
--
--
--
44862
44862
0.0
0.0
--
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)
1.8
1.84
90.6
--
--
--
--
--
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
MOLECULAR REPLACEMENT
1.8
9.98
--
0.0
42578
42578
2284
100.0
0.20573
0.20573
0.20511
0.21735
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
1.8
1.845
2751
163
2800
0.22
0.273
--
90.6
Temperature Factor Modeling
Temperature Factor
Value
Mean Isotropic B
14.21
Anisotropic B[1][1]
0.0
Anisotropic B[1][2]
0.0
Anisotropic B[1][3]
0.0
Anisotropic B[2][2]
0.0
Anisotropic B[2][3]
0.0
Anisotropic B[3][3]
-0.01
RMS Deviations
Key
Refinement Restraint Deviation
r_angle_other_deg
1.603
r_gen_planes_refined
0.008
r_xyhbond_nbd_refined
0.161
r_angle_refined_deg
1.865
r_nbtor_other
0.072
r_symmetry_vdw_other
0.301
r_symmetry_vdw_refined
0.193
r_gen_planes_other
0.004
r_bond_other_d
0.004
r_chiral_restr
0.11
r_scangle_it
4.2
r_symmetry_hbond_refined
0.228
r_bond_refined_d
0.022
r_nbd_other
0.268
r_mcangle_it
1.437
r_nbd_refined
0.215
r_mcbond_it
0.821
r_scbond_it
2.605
r_dihedral_angle_3_deg
12.073
r_dihedral_angle_1_deg
5.394
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms
Numbers
Protein Atoms
2946
Nucleic Acid Atoms
0
Heterogen Atoms
49
Solvent Atoms
539
Software
Software
Software Name
Purpose
HKL-2000
data collection
SCALEPACK
data scaling
AMoRE
phasing
REFMAC
refinement version: 5.0
HKL-2000
data reduction