1M68 | pdb_00001m68

YCDX PROTEIN, TRINUCLEAR ZINC SITE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M65

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.1 M Tris, 60% AS, 5 mM Zinc Acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.35	α = 90
b = 77.35	β = 90
c = 80.05	γ = 120

Symmetry
Space Group	P 3 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	MARRESEARCH		2002-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.9795	APS	22-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	2.3	20	99.2	0.041	33.7	8.5	12703	12596		-3	34

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	2.3	2.35	89.8		0.102	12.8	9.5	757

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1M65	2.3	10	11839	11839	607	100	0.16505	0.16505	0.16181	0.1718	0.22532	RANDOM	38.198

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]
-1.84	-0.92		-1.84		2.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.21
r_scangle_it	14.042
r_scbond_it	12.079
r_mcangle_it	8.163
r_mcbond_it	5.293
r_dihedral_angle_1_deg	4.879
r_angle_refined_deg	1.623
r_nbd_refined	0.244
r_symmetry_vdw_refined	0.242
r_symmetry_hbond_refined	0.226
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.11
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1802
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	13

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
CCP4	phasing