2PAF | pdb_00002paf

Crystal Structure of the Lactose Repressor bound to anti-inducer ONPF in induced state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EFA	pdb entry 1EFA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	281	1.4 M Sodium Acetate, 0.1 M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.541	α = 90
b = 77.541	β = 90
c = 212.456	γ = 90

Symmetry
Space Group	P 41 21 2

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	MAR scanner 300 mm plate	Osmic Blue Max mirrors	2006-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	3.5	20	99.1	0.166	0.166	5.9	4.9	8745	8685	-3	-3

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)
	3.5	3.62	99.5		0.336	0.336	3.5	5

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1EFA	3.5	19.81	8745	8252	413	99.09	0.19856	0.19537	0.19	0.26516	0.2579	RANDOM	28.204

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]
-0.02			-0.02		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.519
r_dihedral_angle_3_deg	22.382
r_dihedral_angle_4_deg	17.799
r_dihedral_angle_1_deg	8.195
r_scangle_it	3.312
r_scbond_it	1.929
r_angle_refined_deg	1.805
r_mcangle_it	1.364
r_mcbond_it	0.964
r_nbtor_refined	0.326
r_nbd_refined	0.27
r_symmetry_hbond_refined	0.221
r_symmetry_vdw_refined	0.208
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.109
r_bond_refined_d	0.018
r_gen_planes_refined	0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4028
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing