1QZ4 | pdb_00001qz4

Structure of YcfC Protein of Unknown Function Escherichia coli

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		MIRAS model built by WARP/ARP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PEG 3350, zinc acetate, lithium acetate , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.102	α = 90
b = 62.749	β = 90
c = 68.399	γ = 90

Symmetry
Space Group	P 21 21 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	CUSTOM-MADE		2003-08-24	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	CUSTOM-MADE		2003-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.999871	APS	19-ID
2	SYNCHROTRON	APS BEAMLINE 19-ID	0.91963	APS	19-ID

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
1,2	1.95	50	82.6	0.107	15.87		13895	11477		-3

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)
	1.95	1.98	36.7		0.423	1.8

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MIRAS	Build by WARP/ARP	2	25	11138	11138		85.24	0.15729	0.15729		0.16		16.821

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]
-0.99			0.8		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	11.153
r_scangle_it	9.392
r_scbond_it	7.548
r_mcangle_it	6.47
r_mcbond_it	5.321
r_dihedral_angle_1_deg	5.268
r_angle_refined_deg	1.582
r_angle_other_deg	0.911
r_metal_ion_refined	0.367
r_symmetry_vdw_other	0.269
r_nbd_other	0.231
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.22
r_symmetry_vdw_refined	0.154
r_symmetry_hbond_refined	0.146
r_chiral_restr	0.091
r_nbtor_other	0.086
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1605
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	15

Software

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