1NPB | pdb_00001npb

Crystal structure of the fosfomycin resistance protein from transposon Tn2921

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	1.6M ammonium sulfate, 100 mM sodium citrate, 5% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.87	68.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 208.597	α = 90
b = 208.597	β = 90
c = 136.358	γ = 90

Symmetry
Space Group	I 4 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113	CCD	ADSC QUANTUM 4		2002-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-D	0.9797	APS	14-BM-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	30	98.9	0.082	20.5	7.3		51262			50.36

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	90.3		0.442	2.7		4613

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1LQO	2.5	12	46761	46761	1433	93.79	0.18457	0.18318	0.23044	RANDOM	31.381

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]
0.46			0.46		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.606
r_scangle_it	3.568
r_scbond_it	2.331
r_angle_refined_deg	1.672
r_mcangle_it	1.403
r_mcbond_it	0.717
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.211
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.12
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6602
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms	92

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing