1P3E | pdb_00001p3e

Structure of Glu endopeptidase in complex with MPD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P3C	PDB ENTRY 1P3C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	0.01 M Tris-HCl buffer, pH 7.0, 2 mM CaCl2, 1.2 M potassium phosphate, 3% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.936	α = 90
b = 55.757	β = 118.17
c = 60.195	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	IMAGE PLATE	MARRESEARCH		1999-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	1.10	EMBL/DESY, HAMBURG	X11

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	1.72	20	93			18778	18778	-2	-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	1.72	1.76	95.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1P3C	1.72	19.69	-3	17769	17769	965	97.34	0.16791	0.16791	0.16579	0.17	0.20809	0.21	RANDOM	13.378

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]
0.84		1.84	-0.23		1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.782
r_scangle_it	3.734
r_scbond_it	2.301
r_mcangle_it	1.557
r_angle_refined_deg	1.42
r_angle_other_deg	1.191
r_mcbond_it	0.877
r_symmetry_vdw_other	0.361
r_symmetry_hbond_refined	0.275
r_nbd_other	0.245
r_symmetry_vdw_refined	0.226
r_nbd_refined	0.183
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.121
r_nbtor_other	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1600
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing