6YTJ | pdb_00006ytj

Magnesium chelatase H subunit (ChlH) E625K 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
3.43	64.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 320.422	α = 90
b = 320.422	β = 90
c = 104.876	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	2.79	80.11	100	0.074	0.993	6.4	5.7		99929

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	2.79	2.86			0.659	0.583	1.2

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6YSG	2.79	80.105	99184	4926	99.25	0.212	0.2089	0.21	0.2676	0.27	Random	61.264

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]
1.225	0.612		1.225		-3.974

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.841
r_dihedral_angle_3_deg	17.609
r_dihedral_angle_4_deg	16.515
r_lrange_it	8.812
r_lrange_other	8.812
r_dihedral_angle_1_deg	6.963
r_mcangle_it	6.02
r_mcangle_other	6.02
r_scangle_it	5.778
r_scangle_other	5.777
r_mcbond_it	3.819
r_mcbond_other	3.819
r_scbond_it	3.585
r_scbond_other	3.584
r_angle_refined_deg	1.381
r_angle_other_deg	1.171
r_nbd_refined	0.207
r_symmetry_xyhbond_nbd_refined	0.186
r_symmetry_nbd_other	0.181
r_nbd_other	0.174
r_nbtor_refined	0.158
r_symmetry_xyhbond_nbd_other	0.153
r_xyhbond_nbd_refined	0.151
r_symmetry_nbd_refined	0.134
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.057
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19393
Nucleic Acid Atoms
Solvent Atoms	19
Heterogen Atoms

Software

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