3LB5 | pdb_00003lb5

Crystal structure of Hit-like protein involved in cell-cycle regulation from Bartonella henselae with unknown ligand

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3IMI	PDB ENTRY 3imi

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	289	PACT screen condition B8, 0.2 M ammonium chloride, 0.1 M MES pH 6.0, 20% PEG 6000, 25% EG as cryo-protectant; crystal tracking ID 202910b8; tag not removed prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.71	α = 90
b = 97.92	β = 90
c = 111.85	γ = 90

Symmetry
Space Group	C 2 2 21

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	RIGAKU SATURN 944+		2009-12-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.9	20	99.1	0.075	17.36	6		75981		-3	26.426

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	1.9	1.95	94.4		0.498	2.3	2.9	5338

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 3imi	1.9	19.47	39631	1982	99.28	0.184	0.182	0.18	0.237	0.24	RANDOM	12.896

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]
-0.34			-0.35		0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.341
r_dihedral_angle_4_deg	14.209
r_dihedral_angle_3_deg	12.26
r_dihedral_angle_1_deg	6.022
r_scangle_it	3.06
r_scbond_it	1.926
r_angle_refined_deg	1.325
r_mcangle_it	1.07
r_mcbond_it	0.609
r_chiral_restr	0.092

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.341
r_dihedral_angle_4_deg	14.209
r_dihedral_angle_3_deg	12.26
r_dihedral_angle_1_deg	6.022
r_scangle_it	3.06
r_scbond_it	1.926
r_angle_refined_deg	1.325
r_mcangle_it	1.07
r_mcbond_it	0.609
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4122
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	36

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.