Experiment: 5LMH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LR2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	296	.3 M sodium tartrate and 50 mM Tris, pH 6.8

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.48	α = 90
b = 58.48	β = 90
c = 151.73	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	296	PIXEL	DECTRIS PILATUS 6M		2015-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.96863	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.96	19.95	93.1	0.143	0.986	5.8	3.2		18364

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.96	2.03	93.4		0.663	0.65	1.9	3.3

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	1LR2	1.96	19.95	17418	923	92.97	0.1808	0.1786	0.18	0.223	0.22	RANDOM	30.245

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]
0.03			0.03		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.54
r_dihedral_angle_4_deg	21.308
r_dihedral_angle_3_deg	14.767
r_dihedral_angle_1_deg	6.842
r_scbond_it	3.739
r_mcangle_it	3.393
r_mcbond_it	2.201
r_angle_refined_deg	1.691
r_chiral_restr	0.121
r_bond_refined_d	0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.54
r_dihedral_angle_4_deg	21.308
r_dihedral_angle_3_deg	14.767
r_dihedral_angle_1_deg	6.842
r_scbond_it	3.739
r_mcangle_it	3.393
r_mcbond_it	2.201
r_angle_refined_deg	1.691
r_chiral_restr	0.121
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1550
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
MOLREP	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.