6QSW | pdb_00006qsw

Complement factor B protease domain in complex with the reversible inhibitor N-(2-bromo-4-methylnaphthalen-1-yl)-4,5-dihydro-1H-imidazol-2-amine.

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		293	2.0 M ammonium sulfate, 0.1 M sodium acetate (pH 4.6), 2 mM inhibitor

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.281	α = 90
b = 91.281	β = 90
c = 260.221	γ = 90

Symmetry
Space Group	P 43 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	PIXEL	DECTRIS PILATUS 2M		2009-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.001	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.64	65.1	95.8	0.068	19.56	7.6		129551

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.7	76.6		0.44	2.52	2.64

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	1.64	65.055	129548	6478	95.837	0.158	0.1567	0.17	0.1881	0.2	21.87

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]
1.028			1.028		-2.056

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.911
r_dihedral_angle_4_deg	17.33
r_dihedral_angle_3_deg	14.239
r_dihedral_angle_1_deg	6.568
r_lrange_it	4.078
r_lrange_other	4.034
r_scangle_it	3.557
r_scangle_other	3.493
r_mcangle_it	3.054
r_mcangle_other	3.054
r_scbond_it	2.905
r_scbond_other	2.849
r_mcbond_it	2.47
r_mcbond_other	2.47
r_rigid_bond_restr	1.72
r_angle_refined_deg	1.405
r_angle_other_deg	1.314
r_nbd_refined	0.199
r_nbd_other	0.195
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.164
r_symmetry_xyhbond_nbd_refined	0.164
r_symmetry_nbd_refined	0.143
r_xyhbond_nbd_refined	0.108
r_ncsr_local_group_3	0.088
r_ncsr_local_group_1	0.08
r_symmetry_nbtor_other	0.077
r_ncsr_local_group_2	0.073
r_chiral_restr	0.069
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6222
Nucleic Acid Atoms
Solvent Atoms	500
Heterogen Atoms	104

Software

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