3DO1 | pdb_00003do1

Thermolysin by Classical hanging drop method before high X-Ray dose on ESRF ID14-2 beamline

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	DMSO, Ammonium sulfate, MES, hanging drop, 293K, pH6.0, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.526	α = 90
b = 92.526	β = 90
c = 128.553	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 4	Toroidal mirror	2007-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.93	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.33	80.13	81	0.243	0.243	3	5.2		64020

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.31	1.38	24.1		0.674	0.67384		1.4	2697

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	PDB ENTRY 1KEI	1.33	68.04	41554	2031	55.53	0.233	0.231	0.23	0.277	0.27	RANDOM	21.019

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]
-0.5	-0.25		-0.5		0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.669
r_dihedral_angle_4_deg	14.543
r_dihedral_angle_3_deg	14.236
r_dihedral_angle_1_deg	5.38
r_scangle_it	2.3
r_scbond_it	1.615
r_angle_refined_deg	1.167
r_mcangle_it	0.916
r_mcbond_it	0.559
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.669
r_dihedral_angle_4_deg	14.543
r_dihedral_angle_3_deg	14.236
r_dihedral_angle_1_deg	5.38
r_scangle_it	2.3
r_scbond_it	1.615
r_angle_refined_deg	1.167
r_mcangle_it	0.916
r_mcbond_it	0.559
r_nbtor_refined	0.305
r_symmetry_hbond_refined	0.255
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.083
r_metal_ion_refined	0.061
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2479
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	22

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

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.