8D9P | pdb_00008d9p

De Novo Photosynthetic Reaction Center Protein Equipped with Heme B and Mn(II) cations

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5VJS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	277	1.2 M Li2SO4, 0.5 M (NH4)2SO4, 150 mM Na citrate, pH 5.9 Cryoprotectant: 28% glycerol, 1.25 M Li2SO4, 0.5 M (NH4)2SO4, 100 mM Na citrate, pH 5.85

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.968	α = 90
b = 44.968	β = 90
c = 238.295	γ = 90

Symmetry
Space Group	P 41 21 2

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	RIGAKU SATURN 944+	Osmic VariMax mirror	2014-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.9	23.25	98.4	0.089	0.093	0.999	22.22	12.6		20059			28.22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95	86.6		0.619	1.66

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 (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	FREE R-VALUE	5VJS	1.9	23.25	19019	1014	98.26	0.22014	0.2189	0.22	0.24336	0.25	RANDOM	37.956

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]
-0.07			-0.07		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.298
r_scangle_other	20.346
r_long_range_B_other	19.72
r_long_range_B_refined	19.628
r_scbond_it	18.459
r_scbond_other	18.377
r_dihedral_angle_3_deg	12.931
r_mcangle_other	10.677
r_mcangle_it	10.671
r_mcbond_it	9.379
r_mcbond_other	9.334
r_dihedral_angle_4_deg	8.474
r_dihedral_angle_1_deg	3.554
r_angle_other_deg	0.976
r_angle_refined_deg	0.943
r_chiral_restr	0.045
r_bond_refined_d	0.005
r_gen_planes_other	0.003
r_gen_planes_refined	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1581
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	46

Software

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