5LOJ | pdb_00005loj

Structure of full length unliganded CodY from Bacillus subtilis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GX5	2GX5, 2B0L
experimental model	PDB	2B0L	2GX5, 2B0L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	1.7M Li2SO4, sodium citrate pH 5.6, 3% dioxane

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.524	α = 90
b = 111.524	β = 90
c = 119.536	γ = 90

Symmetry
Space Group	P 43 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	100	CCD	ADSC QUANTUM 4		2002-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.93300	ESRF	BM14

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	3.7	25	97.5	0.059	33.14	6.1		8235

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	3.7	3.83	98.2		0.408	5.66	6.1

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	2GX5, 2B0L	3.71	24.94	7841	381	97	0.26905	0.26356	0.26	0.38942	0.38	RANDOM	83.452

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]
0.45			0.45		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_rigid_bond_restr	77.221
r_sphericity_bonded	40.899
r_dihedral_angle_2_deg	40.502
r_dihedral_angle_3_deg	26.928
r_scbond_it	23.678
r_scbond_other	23.672
r_mcbond_it	22.974
r_mcbond_other	22.947
r_long_range_B_refined	20.789
r_long_range_B_other	20.789
r_scangle_other	20.667
r_mcangle_other	20.658
r_mcangle_it	20.656
r_dihedral_angle_4_deg	19.582
r_dihedral_angle_1_deg	9.172
r_angle_other_deg	3.421
r_angle_refined_deg	2.135
r_chiral_restr	0.134
r_bond_refined_d	0.018
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4004
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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