2J65 | pdb_00002j65

Structure of LpxC from Aquifex aeolicus in complex with UDP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P42	PDB ENTRY 1P42

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	CRYSTALS OF LPXC WERE GROWN BY HANGING VAPOR DIFFUSION AT 20 DEG C USING 1 UL OF PROTEIN (184 UM) AND 1 UL OF A RESERVOIR SOLUTION CONTAINING 8% PEG 6000, 100 MM TRIS, PH 8.5, AND 300 MM NACL.

Crystal Properties
Matthews coefficient	Solvent content
2.69	53.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.755	α = 90
b = 101.755	β = 90
c = 124.243	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH	PT-COATED MIRRORS, MICROFOCUS BEAMLINE	2006-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.2	50.9	99	0.11	11.3	3.9		36577

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	98.5		0.48	3.6	3.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1P42	2.2	50.9	34736	1836	98.9	0.171	0.168	0.17	0.225	0.22	RANDOM	22.83

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.86	-0.43		-0.86		1.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.024
r_dihedral_angle_4_deg	21.107
r_dihedral_angle_3_deg	14.182
r_dihedral_angle_1_deg	5.973
r_scangle_it	2.701
r_scbond_it	1.671
r_angle_refined_deg	1.34
r_mcangle_it	1.058
r_mcbond_it	0.653
r_nbtor_refined	0.3
r_symmetry_hbond_refined	0.199
r_nbd_refined	0.187
r_symmetry_vdw_refined	0.178
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.105
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4314
Nucleic Acid Atoms
Solvent Atoms	488
Heterogen Atoms	107

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing