1NRZ | pdb_00001nrz

Crystal structure of the IIBSor domain of the sorbose permease from Klebsiella pneumoniae solved to 1.75A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BLE	PDB ENTRY 1BLE cut down to common atoms

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	19-25% PEG 8000, 0.2M ammonium sulphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.848	α = 90
b = 85.311	β = 103.02
c = 67.815	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH	MIRRORS	2001-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ELLIOTT GX-20	1.5418

Data Collection

Overall
ID #	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	1.75	21.38	99.6	0.051	0.051	9.5	2.5	72155	72155			20.16

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.84	99.8		0.235	0.235	3.1	2.4	15789

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 1BLE cut down to common atoms	1.75	21.37	68518	3637	99.65	0.21731	0.21593	0.23	0.24268	0.25	RANDOM	8.907

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]
1.9		0.83	-0.95		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.64
r_dihedral_angle_1_deg	3.996
r_scangle_it	2.769
r_scbond_it	1.648
r_angle_refined_deg	1.346
r_mcangle_it	0.928
r_angle_other_deg	0.722
r_mcbond_it	0.486
r_symmetry_hbond_refined	0.364
r_symmetry_vdw_other	0.362
r_symmetry_vdw_refined	0.303
r_nbd_refined	0.238
r_nbd_other	0.202
r_xyhbond_nbd_refined	0.18
r_xyhbond_nbd_other	0.087
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5148
Nucleic Acid Atoms
Solvent Atoms	468
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing