6QMR | pdb_00006qmr

Complement factor D in complex with the inhibitor (S)-2-(2-((3'-(1-amino-2-hydroxyethyl)-[1,1'-biphenyl]-3-yl)methoxy)phenyl)acetic acid

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	30% PEG MME 2000, 0.1M sodium thiocyanate

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.151	α = 83.69
b = 66.613	β = 64.36
c = 76.377	γ = 74.65

Symmetry
Space Group	P 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		2013-01-01	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)	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	1.54	57.9	84.5	0.072	0.102	0.996	5.82	1.73		142642	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.54	1.63	77.2		0.837	1.18	0.381	0.7	1.59

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	THROUGHOUT	1dsu	2	49.23	63676	3351	87.51	0.2216	0.2198	0.22	0.2555	0.26	RANDOM	21.421

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]
-0.01	-0.13	0.04	0.14	0.05	-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.69
r_dihedral_angle_4_deg	17.992
r_dihedral_angle_3_deg	14.914
r_mcangle_it	4.126
r_mcbond_it	3.31
r_dihedral_angle_1_deg	3.233
r_mcbond_other	3.231
r_angle_other_deg	2.484
r_angle_refined_deg	1.904
r_chiral_restr	0.147

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.69
r_dihedral_angle_4_deg	17.992
r_dihedral_angle_3_deg	14.914
r_mcangle_it	4.126
r_mcbond_it	3.31
r_dihedral_angle_1_deg	3.233
r_mcbond_other	3.231
r_angle_other_deg	2.484
r_angle_refined_deg	1.904
r_chiral_restr	0.147
r_bond_other_d	0.035
r_bond_refined_d	0.016
r_gen_planes_other	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10266
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	168

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.