2HSG | pdb_00002hsg

Structure of transcription regulator CcpA in its DNA-free state

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	3% polyethylene glycol 8000, 100mM CaCl2, 10% (v/v) glycerol, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.464	α = 90
b = 74.464	β = 90
c = 238.923	γ = 120

Symmetry
Space Group	P 61 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	IMAGE PLATE	MARRESEARCH		1997-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.95	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	98.4			14394	14158			66.898

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)
	2.5	2.565	96.1		0.436	3.7

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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1SXH	2.5	30	13447	14158	711	98.26	0.275	0.281	0.271	0.27	0.337	0.34	RANDOM	58.514

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]
1.36	0.68		1.36		-2.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.646
r_dihedral_angle_4_deg	21.272
r_dihedral_angle_3_deg	18.675
r_dihedral_angle_1_deg	8.653
r_mcangle_it	2.191
r_angle_refined_deg	1.616
r_scangle_it	1.551
r_mcbond_it	1.344
r_scbond_it	0.998
r_angle_other_deg	0.809
r_symmetry_vdw_refined	0.36
r_symmetry_vdw_other	0.31
r_nbd_refined	0.279
r_nbd_other	0.237
r_xyhbond_nbd_refined	0.228
r_symmetry_hbond_refined	0.222
r_mcbond_other	0.222
r_chiral_restr	0.118
r_nbtor_other	0.097
r_xyhbond_nbd_other	0.086
r_gen_planes_refined	0.015
r_bond_refined_d	0.014
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2506
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing