2NR9

Crystal structure of GlpG, Rhomboid Peptidase from Haemophilus influenzae

X-RAY DIFFRACTION

---

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, HANGING DROP	6	298	25% PEG4000, 0.1M Citrate, pH 6.0, 0.8M Ammonium Acetate, 15% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.288	α = 90
b = 35.047	β = 104.02
c = 52.931	γ = 90

Symmetry
Space Group	C 1 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	ADSC QUANTUM 210		2005-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11587	ALS	8.3.1

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	2.1	30	94.9	0.048	13.5	1.8	12949	12248		2

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)
1	2.1		93.7		0.59	1.85

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2IC8	2.2	25	10147	10147	513	94.98	0.23591	0.23591	0.23282	0.29535	RANDOM	67.424

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]
-0.27		0.16	0.14		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.219
r_dihedral_angle_3_deg	11.501
r_dihedral_angle_4_deg	8.835
r_dihedral_angle_1_deg	2.586
r_mcangle_it	1.96
r_mcbond_it	1.269
r_scangle_it	1.199
r_scbond_it	1.071
r_angle_refined_deg	0.992
r_symmetry_vdw_refined	0.406
r_nbtor_refined	0.344
r_symmetry_hbond_refined	0.327
r_nbd_refined	0.288
r_xyhbond_nbd_refined	0.229
r_chiral_restr	0.088
r_gen_planes_refined	0.007
r_bond_refined_d	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1529
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	128

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing