6YTN | pdb_00006ytn

Magnesium chelatase H subunit (ChlH) E660W variant from Synechocystis sp.PCC6803

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YSG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	290	0.8-1.2 M sodium citrate and 2 mM dithiothreitol

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 317.55	α = 90
b = 317.55	β = 90
c = 104.43	γ = 120

Symmetry
Space Group	H 3

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		2015-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97630	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	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	2.7	79.39	99.9	0.059	0.997	10.2	5.8		107741

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.77			0.676	0.49	1.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6YSG	2.7	79.387	107741	5365	99.904	0.194	0.1919	0.19	0.2346	0.23	69.301

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]
1.288	0.644		1.288		-4.179

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.834
r_dihedral_angle_3_deg	16.431
r_dihedral_angle_4_deg	15.804
r_lrange_it	8.262
r_lrange_other	8.261
r_dihedral_angle_1_deg	6.734
r_mcangle_it	5.947
r_mcangle_other	5.947
r_scangle_it	5.703
r_scangle_other	5.703
r_mcbond_it	3.844
r_mcbond_other	3.839
r_scbond_it	3.583
r_scbond_other	3.583
r_angle_refined_deg	1.294
r_angle_other_deg	1.143
r_nbd_refined	0.193
r_symmetry_nbd_other	0.176
r_nbd_other	0.164
r_nbtor_refined	0.155
r_xyhbond_nbd_refined	0.141
r_symmetry_xyhbond_nbd_refined	0.122
r_symmetry_nbd_refined	0.117
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.052
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19763
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing