Experiment: 1PD5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CLA	PDB ENTRY 3CLA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	290	methanol,calcium chloride,MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.739	α = 90
b = 129.702	β = 108.38
c = 117.984	γ = 90

Symmetry
Space Group	P 1 21 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	MARRESEARCH	Bent mirror	2002-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.81	EMBL/DESY, HAMBURG	X11

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	2.5	10	99.6	0.065	0.061		3.28	114277	114277	13.91	12.6

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)
	2.5	2.59	99.2		0.291	0.246			9674

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3CLA	2.5	10	2	114277	105347	5537	98.64	0.19912	0.19478	0.28139	RANDOM	46.425

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]
5.92		1.74	-2.96		-1.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.981
r_scangle_it	6.224
r_scbond_it	4.397
r_angle_refined_deg	2.947
r_mcangle_it	2.705
r_mcbond_it	1.509
r_symmetry_hbond_refined	0.418
r_nbd_refined	0.269
r_symmetry_vdw_refined	0.263
r_chiral_restr	0.214

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.981
r_scangle_it	6.224
r_scbond_it	4.397
r_angle_refined_deg	2.947
r_mcangle_it	2.705
r_mcbond_it	1.509
r_symmetry_hbond_refined	0.418
r_nbd_refined	0.269
r_symmetry_vdw_refined	0.263
r_chiral_restr	0.214
r_xyhbond_nbd_refined	0.172
r_bond_refined_d	0.041
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21210
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
AMoRE	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.