6T8V | pdb_00006t8v

Complement factor B in complex with (S)-5,7-Dimethyl-4-((2-phenylpiperidin-1-yl)methyl)-1H-indole

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DLE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	25% PEG3350, 0.1M HEPES PH 7.5, 5 mM inhibitor

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.652	α = 90
b = 97.487	β = 100.465
c = 61.975	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 2M		2012-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.29	60.92	99.1	0.102	0.121	12.22	3.4		28558

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.29	2.36	98.1		0.38	0.45	4.16

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	FREE R-VALUE	1DLE	2.29	48.743	28552	1428	99.153	0.205	0.2023	0.2	0.2539	0.25	24.576

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]
-0.018		-0.072	0.076		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.667
r_dihedral_angle_3_deg	18.529
r_dihedral_angle_4_deg	18.513
r_lrange_it	6.7
r_dihedral_angle_1_deg	6.6
r_scangle_it	4.432
r_mcangle_it	3.291
r_scbond_it	2.86
r_mcbond_it	1.993
r_angle_refined_deg	1.497
r_nbtor_refined	0.313
r_symmetry_nbd_refined	0.224
r_nbd_refined	0.203
r_symmetry_xyhbond_nbd_refined	0.155
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.118
r_ncsr_local_group_1	0.108
r_symmetry_metal_ion_refined	0.047
r_metal_ion_refined	0.013
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4402
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	81

Software

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