3HL1 | pdb_00003hl1

CRYSTAL STRUCTURE OF A FERRITIN LIKE PROTEIN (CC_0557) FROM CAULOBACTER VIBRIOIDES AT 1.95 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.93	293	17.5000% polyethylene glycol 6000, 0.1M citric acid pH 4.93, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.633	α = 90
b = 44.017	β = 96.17
c = 119.381	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-02-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97876,0.97828	SSRL	BL11-1

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	1.95	29.424	96.9	0.039	12.61	3.88		41306		-3	31.69

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	1.95	2.02	94.5		0.501	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.95	29.424	41295	2079	99.2	0.188	0.185	0.19	0.232	0.23	RANDOM	39.863

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]
0.93		1.33	0.48		-1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.978
r_dihedral_angle_4_deg	14.907
r_dihedral_angle_3_deg	13.841
r_scangle_it	6.567
r_scbond_it	4.941
r_dihedral_angle_1_deg	4.703
r_mcangle_it	2.966
r_mcbond_it	2.005
r_angle_refined_deg	1.475
r_angle_other_deg	1.044
r_mcbond_other	0.903
r_symmetry_vdw_other	0.296
r_symmetry_vdw_refined	0.231
r_nbd_refined	0.217
r_nbtor_refined	0.185
r_nbd_other	0.179
r_symmetry_hbond_refined	0.158
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.089
r_nbtor_other	0.085
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4424
Nucleic Acid Atoms
Solvent Atoms	254
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
autoSHARP	phasing
SHELXD	phasing