4QNZ | pdb_00004qnz

Crystal structure of rhomboid intramembrane protease GlpG F146I in complex with peptide derived inhibitor Ac-FATA-cmk

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IC8	PDB ENTRY 2IC8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.5	293	10% PEG 8000, 0.1 M CHES pH 9.5, 0.2 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.94	68.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.4	α = 90
b = 98.4	β = 90
c = 65.26	γ = 120

Symmetry
Space Group	P 63

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 6M-F		2013-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.0	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.55	51.81	98.9			11872	11747	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.64	99.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 2IC8	2.55	51.81	11872	11159	588	98.95	0.2007	0.19941	0.2	0.22406	0.23	RANDOM	45.748

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	-0.03		-0.07		0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.689
r_dihedral_angle_4_deg	17.582
r_dihedral_angle_3_deg	15.748
r_long_range_B_other	9.484
r_long_range_B_refined	9.482
r_dihedral_angle_1_deg	8.083
r_scangle_other	7.331
r_mcangle_it	5.106
r_mcangle_other	5.104
r_scbond_it	4.969
r_scbond_other	4.968
r_mcbond_it	3.573
r_mcbond_other	3.538
r_angle_other_deg	3.233
r_angle_refined_deg	1.514
r_chiral_restr	0.087
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_gen_planes_other	0.009
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1486
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	22

Software

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