3ZMC | pdb_00003zmc

Native structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01, with bound substrate molecule Geranyl pyrophosphate.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZCD	PDB ENTRY 3ZCD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		0.15 M MGCL2, 20% PEG8000, 0.1 M TRISCL PH 8

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.963	α = 90
b = 98.778	β = 90
c = 130.554	γ = 90

Symmetry
Space Group	C 2 2 21

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	ADSC CCD		2012-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.87	40.83	99.9	0.11	9.2	4.9		46143		2	15.5

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	1.87	1.91	100		0.65	1.7	5

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	SIR	THROUGHOUT	PDB ENTRY 3ZCD	1.87	40.86	43687	2275	99.49	0.20711	0.20489	0.22	0.2505	0.26	RANDOM	20.409

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]
1.4			-0.75		-0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.542
r_dihedral_angle_4_deg	18.618
r_dihedral_angle_3_deg	13.926
r_dihedral_angle_1_deg	5.145
r_angle_refined_deg	1.864
r_angle_other_deg	1.286
r_nbd_refined	0.274
r_symmetry_vdw_refined	0.261
r_symmetry_vdw_other	0.233
r_nbd_other	0.215
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.146
r_chiral_restr	0.111
r_nbtor_other	0.099
r_metal_ion_refined	0.095
r_xyhbond_nbd_other	0.088
r_bond_refined_d	0.018
r_gen_planes_refined	0.011
r_bond_other_d	0.007
r_gen_planes_other	0.006
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	4068
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing