1P5D | pdb_00001p5d

Enzyme-ligand complex of P. aeruginosa PMM/PGM

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P5G	PMM/PGM bound to glucose 6-phosphate

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5		Na K tartrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.7	α = 90
b = 74.193	β = 90
c = 84.836	γ = 90

Symmetry
Space Group	P 21 21 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 QUANTUM 4	mirrors	2003-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

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	1.6	25	99.1	0.074	32.1	8.2	59165	58633			18.6

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	1.6	1.66	98.3		0.491	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	rigid body refinement followed by regular refinement	THROUGHOUT	PMM/PGM bound to glucose 6-phosphate	1.6	25	59514	56042	2945	99.15	0.1621	0.1568	0.15565	0.17	0.17901	0.19	RANDOM	14.863

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]
-0.52			-0.42		0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.878
r_scangle_it	3.442
r_scbond_it	2.078
r_angle_refined_deg	1.387
r_mcangle_it	1.268
r_angle_other_deg	0.998
r_mcbond_it	0.692
r_symmetry_vdw_other	0.278
r_symmetry_vdw_refined	0.246
r_nbd_other	0.244
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.162
r_symmetry_hbond_refined	0.14
r_metal_ion_refined	0.09
r_chiral_restr	0.085
r_nbtor_other	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3436
Nucleic Acid Atoms
Solvent Atoms	464
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing