1GN9 | pdb_00001gn9

Hybrid Cluster Protein from Desulfovibrio desulfuricans ATCC 27774 X-ray structure at 2.6A resolution using synchrotron radiation at a wavelength of 1.722A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1E2U	PDB FROM ENTRY 1E2U, EXCLUDING ALL CLUSTER ATOMS AND SOLVENT MOLECULES

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6	293	25% PEG 4000, 0.1M MES PH6.0, T=293K, pH 6.00

Crystal Properties
Matthews coefficient	Solvent content
2.03	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.4	α = 82.7
b = 61.8	β = 73.7
c = 72.2	γ = 87.3

Symmetry
Space Group	P 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	COLLIMATING AND FOCUSING MIRROR	2000-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.6	30	95.9	0.08	4.2	4.1		27761			18.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.69	94.5		0.13	2.6	4.1

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	IRON ANOMALOUS AND MOLECULAR REPLACEMENT	THROUGHOUT	PDB FROM ENTRY 1E2U, EXCLUDING ALL CLUSTER ATOMS AND SOLVENT MOLECULES	2.6	25.01	27982	732	96.3	0.193	0.193	0.19	0.26	0.26	RANDOM	10.9

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]
0.73	0.12	-2.94	-0.38	0.4	-0.35

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.3
c_scangle_it	5.38
c_mcangle_it	4.64
c_scbond_it	3.79
c_mcbond_it	2.99
c_improper_angle_d	2.38
c_angle_deg	1.3
c_bond_d	0.013
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8173
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	31

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing