4JYF | pdb_00004jyf

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	pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.641	α = 90
b = 78.762	β = 90
c = 86.088	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	PIXEL	DECTRIS PILATUS 6M			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.976	ESRF	ID29

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	1.45	60	99.1	0.053			117963	116913

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	1.45	1.54	96.4

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 (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	1.45	58.12	58494	58494	3119	99.75	0.13451	0.13284	0.1319	0.16613	0.1631	RANDOM	13.8

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]
1.33			-0.31		-1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.116
r_dihedral_angle_1_deg	18.333
r_dihedral_angle_4_deg	15.221
r_dihedral_angle_3_deg	11.787
r_sphericity_free	5.425
r_scangle_it	3.281
r_sphericity_bonded	2.781
r_scbond_it	2.457
r_mcangle_it	1.735
r_rigid_bond_restr	1.732
r_angle_refined_deg	1.723
r_angle_other_deg	1.432
r_mcbond_it	1.232
r_mcbond_other	0.501
r_symmetry_vdw_other	0.277
r_nbd_refined	0.265
r_nbd_other	0.209
r_symmetry_vdw_refined	0.191
r_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.18
r_symmetry_hbond_refined	0.155
r_chiral_restr	0.11
r_nbtor_other	0.085
r_bond_refined_d	0.013
r_bond_other_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2729
Nucleic Acid Atoms
Solvent Atoms	380
Heterogen Atoms	196

Software

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