4DCZ | pdb_00004dcz

Crystal structure of a domain from a mycoplasma genitalium terminal organelle protein

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	22% PEG 2000, 0.1 M SODIUM CITRATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.003	α = 90
b = 81.003	β = 90
c = 73.297	γ = 120

Symmetry
Space Group	P 31 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	ADSC QUANTUM 315r	MIRRORS	2009-07-26	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315r	MIRRORS	2009-11-01	M	SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.979	ESRF	ID14-4
2	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.979	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.9	30	74	0.067	0.066	32.7	10.5		6450		-3	70

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	2.9	3	90		0.498	0.393	5.2	10

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.9	27.18	6418	294	99.8	0.206	0.203	0.2	0.26	0.26	RANDOM	62.51

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]
0.22	0.11		0.22		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.461
r_dihedral_angle_4_deg	31.237
r_dihedral_angle_3_deg	19.302
r_dihedral_angle_1_deg	7.571
r_scangle_it	3.086
r_scbond_it	1.902
r_angle_refined_deg	1.705
r_mcangle_it	1.356
r_angle_other_deg	0.935
r_mcbond_it	0.706
r_mcbond_other	0.131
r_chiral_restr	0.091
r_bond_refined_d	0.02
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	922
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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