4JYD | pdb_00004jyd

X-ray snapshots of possible intermediates in the time course of synthesis and degradation of protein-bound Fe4S4 clusters.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	100 mM Tris; 200 mM Li2SO4; 30% PEG4000, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.598	α = 90
b = 78.699	β = 90
c = 85.96	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					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.71	60	96			71684	68817

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.71	1.8	85.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.71	43.6	35223	35223	1879	98.26	0.1924	0.19239	0.18935	0.1933	0.25056	0.2533	RANDOM	15.845

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]
0.49			0.37		-0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.628
r_dihedral_angle_4_deg	19.086
r_dihedral_angle_3_deg	13.324
r_sphericity_free	6.36
r_dihedral_angle_1_deg	6.125
r_scangle_it	3.416
r_scbond_it	2.556
r_sphericity_bonded	2.479
r_angle_refined_deg	1.843
r_rigid_bond_restr	1.791
r_mcangle_it	1.734
r_mcbond_it	1.252
r_angle_other_deg	0.988
r_mcbond_other	0.473
r_symmetry_vdw_other	0.257
r_xyhbond_nbd_refined	0.222
r_nbd_refined	0.221
r_symmetry_hbond_refined	0.218
r_nbd_other	0.213
r_symmetry_vdw_refined	0.207
r_nbtor_refined	0.181
r_chiral_restr	0.106
r_nbtor_other	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2730
Nucleic Acid Atoms
Solvent Atoms	368
Heterogen Atoms	195

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling