2PMU

Crystal structure of the DNA-binding domain of PhoP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KGS	PDB entry 1KGS C-terminal domain

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.6	298	1.4 M Na/K phosphate, pH 5.6, 100 mM glycine, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.884	α = 90
b = 101.129	β = 126.72
c = 86.93	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 210		2006-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.9795	NSLS	X6A

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	1.779	20	94.8	0.036	18.6	2.9		65220

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	1.779	1.84	96.7		0.582	2.03	2.7	6629

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1KGS C-terminal domain	1.779	20	65210	3310	94.63	0.198	0.196	0.238	RANDOM	41.509

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]
0.35		0.43	-0.48		0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.006
r_dihedral_angle_4_deg	19.734
r_dihedral_angle_3_deg	15.73
r_dihedral_angle_1_deg	5.719
r_scangle_it	4.449
r_mcangle_it	3.729
r_scbond_it	3.185
r_mcbond_it	2.594
r_angle_refined_deg	1.554
r_metal_ion_refined	0.378
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.266
r_nbd_refined	0.236
r_symmetry_hbond_refined	0.186
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.117
r_symmetry_metal_ion_refined	0.115
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4796
Nucleic Acid Atoms
Solvent Atoms	489
Heterogen Atoms	46

Software

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