3I4D | pdb_00003i4d

Photosynthetic reaction center from rhodobacter sphaeroides 2.4.1

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	292	1M Potassium Phosphate, 90mM Sodium Chloride, 3% w/v Heptanetriol, 2% w/v Hexanetriol, 3% w/v Dioxane, 0.05% w/v LDAO, 10mM TRIS-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292.0K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 138.8	α = 90
b = 138.8	β = 90
c = 184.569	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	MAR CCD 165 mm	Mirrors	2006-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW14A	0.954	Photon Factory	AR-NW14A

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	2.01	30.254	95.6	0.058	21.3	7.3	130897	130897			33.61

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.01	2.08	67.1		0.502	1.7	2.9	9061

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 (All)	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	2.01	30.25	117829	117829	6134	90.93	0.18253	0.18124	0.18124	0.21	0.20658	0.22	RANDOM	42.99

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]
0.35	0.18		0.35		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.91
r_dihedral_angle_4_deg	18.895
r_dihedral_angle_3_deg	13.383
r_dihedral_angle_1_deg	5.479
r_scangle_it	3.531
r_scbond_it	2.58
r_angle_refined_deg	1.922
r_mcangle_it	1.626
r_angle_other_deg	1.037
r_mcbond_it	0.976
r_mcbond_other	0.305
r_symmetry_vdw_other	0.273
r_nbd_refined	0.226
r_symmetry_vdw_refined	0.21
r_nbtor_refined	0.203
r_nbd_other	0.199
r_xyhbond_nbd_refined	0.184
r_symmetry_hbond_refined	0.171
r_chiral_restr	0.122
r_nbtor_other	0.092
r_metal_ion_refined	0.066
r_bond_refined_d	0.019
r_gen_planes_refined	0.011
r_symmetry_metal_ion_refined	0.01
r_bond_other_d	0.004
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
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	6464
Nucleic Acid Atoms
Solvent Atoms	553
Heterogen Atoms	1228

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling